Population genetics studies provide valuable information about the patterns of connectivity and range expansion of African frugivorous fruit flies. Human-mediated movements related to trade of commodities and transport are generally indicated as one of the primary mechanisms by which tephritid pests expand their contemporary and historical ranges. This results in complex colonisation dynamics, as suggested for the widely distributed pests Bactrocera dorsalis s.s. and Zeugodacus cucurbitae, and for the cosmopolitan pest of African origin Ceratitis capitata. Analysis of the population structure of African fruit flies can also reveal cryptic genetic structures and incipient speciation, as observed for the Ceratitis FAR complex (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa) and the mango fruit fly, Ceratitis cosyra. Here we provide a synthesis of the current knowledge about the population structure of the main frugivorous fruit flies that are pests in Africa.