This chapter presents an analysis of the results for more than a decade of research conducted in forests and homegardens of Yucatan, Mexico. Species native to this region, such as Cordia dodecandra (Chak k’oopte’), Brosimum alicastrum (Ox), and Spondias purpurea (Abal), are grown in homegardens under management practices that may induce phenological, phenotypic, and genetic changes. Adult individuals from two remnant forests and homegardens in two municipalities of the state of Yucatan were studied based on phenological monitoring and distribution modeling of these three species. In addition, seed germination and seedling survival of C. dodecandra were evaluated, as well as the incidence of visible leaf damage by herbivores and fungi. The karyotype was also characterized, and forage production of B. alicastrum was evaluated, and the morphological variation of S. purpurea fruits was analyzed. Recognizing the nutritional, timber, and forage value of the three species, families grow and manage them in their homegardens, providing them with shelter and protection. In such systems, these three species have found a microhabitat suitable for survival and reproduction, in contrast to their increasingly fragmented natural habitat.