A set of 74 specimens of Ceratitis capitata from six sampling sites (3 > n > 19), collected across five African countries, from 2006 to 2011, were subjected to genotyping by sequencing (GBS) and their phylogeographic and population structure investigated. The analysis of 14,524 filtered SNPs revealed weak genetic structuring with differences occurring regionally and mainly between North Africa (Morocco) and Sub-Saharan Africa geographic collections. Minor genetic differentiation was also observed between populations from East and West Africa. The relatively weak structuring suggests that, at African continental scale, medfly populations are interconnected by substantial gene flow and that human mediated processes, including fruit production and trade, play a fundamental role in the observed patterns. GBS and alignment to the draft genome of C. capitata, allowed identifying a first panel of SNPs for the resolution of populations from North and Sub-Saharan Africa and a second for populations from East and West Africa. These SNPs will be further tested with the objective of developing molecular tools for the source estimation of African interceptions.