Latin America is thought to be the world’s most biodiverse region, but as in the rest of the world, the number of species and the size of their populations is generally in sharp decline. Most experts consider agriculture to be the most important cause of biodiversity decline. At one extreme of policy argument regarding biodiversity conservation are those who argue that the only path to species protection is the establishment of many more and larger “protected areas” in which human activities will be severely restricted. On the remaining land agriculture will be carried out largely with the presently prevailing methods of “industrial agriculture,” including heavy reliance on synthetic pesticides and fertilizers, heavy machine use, large-scale irrigation schemes, limited crop diversity, and crops genetically engineered to maximize returns from these tools and techniques. Those who argue for these policies largely accept that industrial agriculture of this sort is severely hostile to biodiversity, but argue that the high productivity of such methods makes it possible to limit agriculture to a relatively small land base, leaving the rest for protected areas and other human activities. On the other side of the argument are those who argue that agricultural techniques are either available or can be created to make agricultural areas more favorable to species survival. They argue that even with a desirable expansion of protected areas, such reserves cannot successfully maintain high biodiversity levels if protected reserves are not complemented by an agriculture more friendly to species survival and migration. The policy arguments on these issues are of major human and biological importance. They are also very complex and depend on theoretical perspectives and data that do not provide definitive guidance. One way to enrich the debate is to develop a specifically historical perspective that illuminates the relationship between human actions and species diversity. In Latin America, humans have been modifying landscapes and species composition of landscapes for thousands of years. Even in areas of presently low human population density and extraordinarily high species diversity, such as remaining tropical rainforests, humans may have been active in shaping species composition for millennia. After 1492, human population levels in Latin America plummeted with the introduction of Old-World diseases. It is often assumed that this led to a blossoming of species diversity, but the historical evidence from 1492 to the present strongly suggests the combination of European technologies and the integration of agriculture into world markets meant more damaging use of soils, widespread deforestation, and subsequent decline in species numbers. The exploitation and consequent despoliation of Latin American resources were integral to colonialism and intensified later by national governments focused on rapid economic growth. High species diversity remained in areas that were too difficult to exploit and/or were used by indigenous populations or smallholders whose production techniques were often favorable to species survival. Many of these techniques provide clues for how agriculture might be reshaped to be more friendly both to biodiversity and social equity.