Humans have domesticated diverse species from across the plant kingdom, yet much of our foundational knowledge of domestication has come from studies investigating relatively few of the most important annual food crops. Here, we examine the impacts of domestication on genetic diversity in a tropical perennial fruit species, mango (Mangifera indica). We used restriction site associated DNA sequencing to generate genomic single nucleotide polymorphism (SNP) data from 106 mango cultivars from seven geographical regions along with 52 samples of closely related species and unidentified cultivars to identify centers of mango genetic diversity and examine how post-domestication dispersal shaped the geographical distribution of diversity. We identify two gene pools of cultivated mango, representing Indian and Southeast Asian germplasm. We found no significant genetic bottleneck associated with the introduction of mango into new regions of the world. By contrast, we show that mango populations in introduced regions have elevated levels of diversity. Our results suggest that mango has a more complex history of domestication than previously supposed, perhaps including multiple domestication events, hybridization and regional selection. Our work has direct implications for mango breeding and genebank management, and also builds on recent efforts to understand how woody perennial crops respond to domestication.