Central Asia is an important center of origin for many globally valued fruit and nut tree species. Forest degradation and deforestation are cause for concern for the conservation of these valuable species, now confined to small remnant populations. Home gardens have the important function of sustaining household food consumption and income generation, and can potentially play a critical role in conserving diversity of fruit and nut trees. These systems have been very poorly documented in the scientific literature. This study contributes to filling this gap by describing the diversity of fruit and nut trees in home gardens of Kyrgyzstan, Uzbekistan, and Tajikistan, examining their dynamic flow of planting material and its sources, understanding their future prospects, and looking at significant differences between the three countries. Home gardens show a similar portfolio of the most abundant tree species (apple, apricot, walnut, pear, and plum). Although the diversity of tree species and varieties recorded is significant, small population sizes can limit future possibilities for this diversity to thrive, given the pressure on natural stands and on habitats where the preferred species are found. Furthermore, the selection of species and varieties to be planted in home gardens is increasingly influenced by market opportunities and availability of exotic material. Some of the most abundant tree species recorded are represented largely by exotic varieties (apple, pear), while others (e.g., apricot, walnut, plum) are still mainly characterized by traditional local varieties that are not formally registered. Home gardens continue to play a critical role in rural livelihoods and in national economies, and many rural inhabitants still aspire to maintain them. Thus, home gardens should be integrated in national research and extension systems and closely linked to national conservation efforts. Changes and possible declines in the diversity they host, their health status, and resilience should be carefully monitored.