Arnold, 2004 Kovach et al., 2007 Purugganan & Fuller, 2009 Meyer & Purugganan, 2013 Olsen & Wendel, 2013 The International Peach Genome Initiative, 2013 Washburn et al., 2016). As such, the domestication process provides tractable systems in which to study convergent evolution, gene flow, adaptation, diversification and genome evolution (e.g. The process of crop domestication is a special case of co-evolution that gradually increases plant–human interdependence, and results in various levels of intensity of cultivation and breeding (Clement, 1999 Zeder, 2006 Pickersgill, 2007). Over the past 12 000 yr, humans have domesticated thousands of species from across the plant kingdom (Meyer et al., 2012 Meyer & Purugganan, 2013 Gaut et al., 2015). 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. Our results suggest that mango has a more complex history of domestication than previously supposed, perhaps including multiple domestication events, hybridization and regional selection.By contrast, we show that mango populations in introduced regions have elevated levels of diversity. We found no significant genetic bottleneck associated with the introduction of mango into new regions of the world. We identify two gene pools of cultivated mango, representing Indian and Southeast Asian germplasm.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.Here, we examine the impacts of domestication on genetic diversity in a tropical perennial fruit species, mango ( Mangifera indica). 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.