The political boundaries of Chile follow relatively natural biogeographic boundaries. To the north is the hyperarid Atacama Desert. The Tacna-Arica region, located along the Peruvian border, experiences the most extreme conditions. Here, a virtual absence of rainfall separates the Peruvian floristic elements of the desert from the Chilean elements. To the east, the Mediterranean-climate region of central Chile is strongly delineated by the high Andean Cordillera. Many peaks in this range reach well above 6,000 m, shielding Chile from weather fronts moving westward across Argentina.

Although major uplift of the Andes began in the mid-Tertiary, at least 14 million years ago, the range remains tectonically active today. The elevation of mountain passes along the Andes in northern and central Chile are too high to allow easy migration of either plants or animals, and thus have helped to isolate Chile’s flora and fauna. Only in southern Chile, where the Andes are lower, have mountain-crossing migrations occurred. The severe cold of Patagonia strongly reduces the biological diversity of southern Chile.

Comparisons of species diversity between Chilean organisms and those of other Mediterranean-climate regions deserve some caution in terms of the areas included. As with California, the political boundaries of Chile include desert and wet forest ecosystems that are not comparable with core Mediterranean-climate habitats. Most figures for Chilean diversity in the literature are based on political boundaries. An additional issue of political boundaries comes in assessing levels of endemism for the Chilean flora or fauna. Levels of endemism for all groups are much lower if strict adherence to the political boundaries of Chile rather than the more natural boundaries of the Chilean/Patagonian biogeographic province.

Much of central Chile, which covers an area of about 14,000 square kilometers, has a physiographic structure parallel to that of California. Moving inland from the Pacific Ocean, there is a coastal range of mountains, a broad central valley, and a high mountain range to the east. The geologically recent Cordillera de la Costa is relatively tall. West of Santiago, at about 331 S latitude, the major peaks are Cerro Campana (1,910 m), Campanita (1,510 m), and El Roble (2,220 m). These mountains are high enough to intercept moisture from humid southwestern winds, producing woodland areas with significant fog interception and thus improved water relations.

The dominant vegetation in central Chile is matorral, an evergreen shrubland similar in general form to chaparral. Along the coast and to the north this community grades into a coastal matorral with a greater dominance by drought deciduous shrubs. At higher elevations and on sites with greater water availability, matorral grades into a sclerophyll woodland community, and to the south into hygrophilopous woodlands with many species characteristic of the Valdivian forest region. Much of the central valley of Chile today is dominated by a savanna community termed espinal, with Acacia caven as the sole dominant. This community is almost certainly the result of human intervention on landscape processes over the last four centuries. Sclerophyll woodland and matorral would once have covered much of this area.

Unlike California and the Mediterranean Basin, the high mountains of the Andean Cordillera in central Chile do not have a forest zone. The young age of these mountains and lack of soil weathering has produced unstable geological conditions on the west-facing slope of the Andes. Matorral communities on the lower foothills of the Andes give way to a low and scrubby montane matorral community at about 2000 m elevation.

The biological diversity of Chile dates back to the ancient supercontinent of Gondwanaland. Southern Chile in particular exhibits many broad biogeographical linkages with New Zealand and Australia. Central Chile shows other biogeographical connections with southeastern Brazil, a linkage dating back to mid-Tertiary times before the uplift of the Cordillera de los Andes. Since the Andean uplift, however, the biota of Chile has evolved largely in isolation from other biogeographic regions.

Biosystematic and biogeographic knowledge of the flora and fauna of Chile has increased greatly in recent decades, and thus the biodiversity of most groups of vascular plants and vertebrates is relatively well known. These syntheses have been applied more generally to the country as a whole, however, rather than to discrete regional areas. Thus, there is a strong need for more regional studies that evaluate patterns of alpha, beta, and gamma diversity in relation to environmental gradients.

The age and evolutionary isolation of the Chilean flora is clearly indicated by the large number of families that are largely endemic to the Chilean floristic region, which includes adjacent areas of austral forest in southern Argentina. One family of ferns, the Thyrsopteridaceae, and 10 families of Angiosperms are endemic to Chile in a broad florisitic context that extends past political boundaries.

Endemic families entirely restricted to Chile are the Aextoxicaceae and Gomortegaceae of central Chile, and Lactoridaceae restricted to the Juan Fernandez Islands. Other families that are largely Chilean in distribution but cross political boundaries into desert areas of Peru or Austral forests of southern Argentina, are the Malesherbiaceae, Misodendraceae, Vivianiaceae, and Francoaceae. Of these endemic families, the monotypic Aextoxicaceae and Gomortegaceae have distributions centered in the Mediterranean-climate regions of central Chile, while the Malesherbiaceae is centered in the coastal deserts and adjacent arid montane regions of northern Chile and southern Peru.

For continental Chile as a political unit, the vascular plant flora consists of about 4600 native species, divided into about 850 native genera and 180 families. This flora includes 124 species of ferns and fern relatives, 13 species of gymnosperms, and slightly more than 4500 species of Angiosperms. The flora of central Chile, excluding the desert areas north of La Serena, the Juan Fernandez Islands, and the forest and moorland areas south of Concepción, is estimated to be about 2400 species. The current concept of the biodiversity ‘‘hotspot’’ of central Chile has been recently expanded well beyond the Mediterranean-climate regions to include the Atacama Desert, Juan Fernandez Islands, and the Valdivian forest region. Thus, under this greatly expanded definition, the flora includes 3539 species.

Endemism is high at the generic level in the Chilean flora. Extrapolating from the literature, 16 percent of Chilean genera are strict endemics restricted to the political boundaries of the country. Another 17 percent of the genera are endemic to Austral regions of Chile and adjacent areas of Argentina. Together, then a third of the genera are endemic to the Chilean-Patagonian floristic province. Twenty-two percent of the genera have broad South American patterns of distribution, while 10 percent have Gondwanaland origins with extant species in New Zealand and/or Australia.

The levels of species-level endemism within groups of the Chilean flora are high, but the values reported vary somewhat depending on whether or not the author is quoting distributions within the strict political boundaries of Chile. A more natural view of endemism would include Andean species or austral forest and moorland species that occur within communities of the Chilean-Patagonian biogeographic province that may extend into Argentina. Using the political boundaries of Chile, one authority estimated that 62 percent of the vascular plant species were endemic, while others estimate about 50–55 percent. A rich flora high in endemism occurs on the oceanic Juan Fernandez Islands which lie about 500 km off the central Chilean coast and contain floristic elements from both the mainland of Chile and Polynesia. The
flora includes 361 species of vascular plants, of which 60 percent are endemic.

The 20 largest genera of Chilean vascular plants make up about 30 percent of the flora. This group is led by Senecio (Asteraceae) with 218 species, Adesmia (Fabaceae) with 140 species, Oxalis (Oxalidaceae) with 111 species, Calceolaria (Scrophulariaceae) with 86 species and Calandrinia sensu latu (Portulacaceae) with 70 species. As might be expected, the degree of endemism within the largest families is higher than that for the flora overall. Eleven of the 20 largest families have 80 percent or more of their species endemic to Chile. These numbers on species diversity and endemism will no doubt change to some extent as these large and difficult genera become better studied. One of the most charismatic of endemic species is the Chilean wine palm, Jubaea chilensis. This large palm was once widespread through central Chile but is much more restricted in distribution today.

Mammal diversity in Chile, as in other parts of temperate South America, is low. Severe climatic conditions associated with Pleistocene glacial movements in the Andes may have had a strong impact in reducing the diversity of temperate mammal faunas in South America. Major faunal extinctions also occurred in at the end of the Pleistocene in both South America and North America, and these extinctions have been associated with the arrival of early man.

Many ecological niches in temperate South America appear to be incompletely occupied by mammals in comparison with North America. Chile has 99 native terrestrial mammal species, 64 of which occur within the hotspot region. Five genera are endemic. The largest single group is the Rodentia (60%). Next in abundance are the Carnivora with 14%, and the Chiroptera (bats) with 10%. Few large mammal species exist. These include species of felids (puma, Geoffrey’s cat, and colo colo), three species of canids (all fox species of Pseudalopex), four camelids (guanaco, vicuna, and the domesticated llama and alpaca), and three cervids (huemul, northern huemul, and pudu). The mammal fauna of Chile are associated with five biogeographic areas: the summer rainfall Altiplano region of northeastern Chile, the Atacama Desert and adjacent winter rainfall Andes of northern Chile, the Andes of central Chile, the Mediterranean-climate region of central Chile, the Austral forests of southern Chile, and the Patagonian region.

In addition, 15 species of terrestrial mammals  have become naturalized in Chile. Five of these occur only on the Juan Fernandez Islands, where they have greatly disrupted the structure and composition of the native flora.

The two native marsupials of Chile are part of the its legacy as a former remnant of Gondwana, ancestral home of all marsupials. Most notable is the diminutive monito del monte (Dromiciops gliroides) belongs to the most ancient  lineage of marsupials alive today. In fact, this species constitutes its own an endemic family, the Microbiotheriidae. It is found in Chile’s winter-rainfall Valdivian forests.

The total bird diversity of Chile is only moderate. Including the oceanic islands of Pascua and Juan Fernandez and the Antarctic territory claimed by Chile, there are reports of 451 native species and five introduced species for Chile. The hotspot area includes 226 species, with 12 of these being endemic. The biogeographical isolation of the Chilean bird fauna shows parallels with that of the mammal fauna in the manner in which niches have been filled in unusual manners. Corvids, for example, are absent from Chile. Their role as scavengers has been filled by caracaras.

The 87 native species of terrestrial reptiles in Chile are divided into 7 families and 18 genera. These include six snakes (four genera) and 81 lizards (14 genera). Within the hotspot boundaries there are 41 reptile species, with 27 of these being endemic.

The diverse lizard fauna of Chile is strongly dominated by the family Tropiuridae, in particular the iguanid genus Liolaemus. This diverse genus and its evolution have been the focus of a large number of ecological and evolutionary studies. The occurrence of distinctive populations within individual species has led to the designation of a large number of subspecies. There are two endemic species of snakes. The highest diversity of reptiles in Chile occurs in the northern desert and Andean areas, outside of the core Mediterranean-climate region. These areas are also the site of the greatest degree of reptile endemism.

The amphibian fauna of Chile exhibits an unusually high level of endemism in comparison with other vertebrate groups. There are 43 native species in the hotspot of central Chile,  5 of the 12 genera being endemic. The centers of amphibian diversity in the region are the forests of south-central Chile. Only frogs and toads are native to the region; salamanders are conspicuous by their absence. More than three-quarters of these species are endemic to Chile, many of them rare and localized in distribution.

The native fish of Chile’s hotspot region number 43 species, including two endemic families.

The first human settlers arrived in what is now coastal Chile roughly 4,000 years ago. The Araucanian culture eventually became the largest indigenous group in Chile. This society of hunters, gatherers, and farmers lived in small villages and employed irrigation in central Chile. Human impact on the area remained relatively low in the precolombian era. But the arrival of the Spanish conquistadors in the early sixteenth century, however, led to rapid agricultural expansion and landscape clearance for grazing by goats and cattle. A lack of forested areas has led to four centuries of widespread cutting of matorral shrubs to produce charcoal for fuel.