Tropical home gardens are widely recognized as reservoirs of biodiversity. Typically, Maya home gardens have an area of intensive management and one of extensive management. In the latter, some wild plant species may find safe sites for establishment, since they exhibit a high degree of similarity (in terms in plant species composition) to the surrounding forest and are dominated by plants with fleshy fruit. Therefore, this may attract frugivorous animals, which in turn may generate some seed rain. The objective of our study was to compare seed rain in the extensively managed areas of home gardens and in the surrounding forest during the fruiting peak in a rural landscape in the Yucatan. We assessed seed rain using seed traps in two habitats: the extensively managed areas of home gardens and an adjacent tropical forest. Seed rain was more abundant, denser and more diverse in the home gardens than in the adjacent forest. Approximately one quarter of the seeds recorded are from species shared between the forest and home gardens, suggesting there is notable seed exchange between these habitats. Also 50% of the seed species exclusively found in home gardens are allochthonous, likely rare species from the forest. In general, our results suggest that home gardens—particularly their extensively managed areas—are effective seed traps for forest species.