The Madrean Pine-Oak Woodlands are home to about 5,300 species of flowering plants, a quarter of the Mexican flora. Although it is difficult to gauge the level of endemism because of the incompleteness of inventories, high-end estimates suggest that as many as 75 percent of these species may be found nowhere else on Earth. The real percentage is probably rather lower than this, but certainly still high.
Mexico is an important center of diversity for both pines and oaks, with 44 of the 110 recognized pine species and over 135 species of oak, more than 30 percent of the world's species in this genus. Of these oak species, more than 85 are endemic to Mexico. Two endemic species of oak are found only in the Sierra Madre Occidental, the Endangered Mexican Oak (Quercus carmenensis) and Vulnerable Q. deliquescens.Forests in the Baja California Peninsula have an important diversity of pine trees, including the Sugar Pine (Pinus lambertiana), which can grow as high as 70 meters and produces pine cones 70 centimeters in length.
Roughly 525 bird species are found in the Madrean Pine-Oak Woodlands, of which more than 20 are endemic to the hotspot. Most of these endemics occur in the middle Sierra Madre Occidental, the Trans-Mexican Volcanic Belt and the southern Sierra Madre Oriental.
Threatened species found in the hotspot include the the Critically Endangered short-crested coquette (Lophornis brachylophus), Endangered blue-capped hummingbird (Eupherusa cyanophrys), Vulnerable white-tailed hummingbird (E. poliocerca) and Vulnerable dwarf jay (Cyanolyca nana). The imperial woodpecker (Campephilus imperialis), currently listed as Critically Endangered and once the largest woodpecker in the world, is now almost certainly extinct. The slender-billed grackle (Quiscalus palustris), once endemic to the marshlands around Mexico City, was driven to extinction early last century.
Of the three bird genera endemic to the hotspot, two are monotypic: Euptilotis, represented by the eared quetzal (E. neoxenus), and Xenospiza, represented by the Endangered Sierra Madre sparrow (X. baileyi, EN). The third endemic genus, the remarkable Rhynchopsitta parrots, has two species, the Endangered thick-billed parrot (R. pachyrhncha) and the Endangered maroon-fronted parrot (R. terrisi).
Nearly 330 mammals are thought to occur in the hotspot, although only six are endemic. Even with so few endemic species, there are two endemic genera, both monotypic: Zygogeomys, represented by the Endangered Michoacán pocket gopher (Z. trichopus), and Romerolagus, represented by the Endangered volcano rabbit (R. diazi). The volcano rabbit, which is endemic to the Trans-Mexican Volcanic Belt surrounding Mexico City, is one of the world's smallest and most unusual rabbits. It has small, round ears and, unlike other rabbits, makes high-pitched penetrating sounds.
More than 380 species of reptiles occur in the Madrean Pine-Oak Woodlands, nearly 40 of which are endemic. There is also one endemic reptile genus, Rhadinophanes, which is represented by a single species, the graceful mountain snake (R. monticola).
Among lizards, there are 50 species of the genus Sceloporus, six of which are endemic, and 14 species of Anolis, two of which are endemic. The Colubridae family of snakes is also particularly well represented, with nearly 150 species, more than 15 of which are endemic.
Amphibian diversity in the hotspot is remarkable, with nearly 200 species, about 50 of which are endemic. Among frogs, there are 38 species of Hyla, with nine endemics, and 34 species of Eleutherodactylus, with seven endemics. Among salamanders, which are typically restricted to northern temperate zones, the hotspot holds 63 species in the family Plethodontidae, with 27 endemics, and 13 species from the family Ambystomatidae, with five endemics.
Surprisingly, given the "sky island" characteristic of much of the hotspot, there are more than 80 fish species present here, nearly 20 of which are endemic. This is in part due to the fact that Mexico's overall fish fauna is extremely diverse, even at high elevations and in semi-arid regions. Many of these species come from the minnow family Cyprinidae. In central Mexico, the fauna is composed mostly of lake-adapted fishes in high-elevation lakes that were created by tectonic plate activity and volcanism. These species include several live-bearing fishes in the family Goodeidae and a number of silversides in the endemic Mexican genus Chirostoma.
The best-known invertebrates in the Madrean Pine-Oak Woodlands are the hotspot's approximately 160-200 butterfly species, of which about 45 are endemic. Perhaps the most spectacular feature pf the hotspot's invertebrate fauna is the annual overwintering of millions of monarch butterflies (Danaus plexippus) in the pine forests of Michoacán.