Sixteen new polymorphic microsatellite loci were developed for the three species of the Ceratitis FAR complex (C. rosa, C. fasciventris and C. anonae) and their optimal amplification conditions characterised. These markers were tested on six field populations of the three fruit flies sampled in different African countries. After Bonferroni corrections, allele frequencies supported Hardy-Weinberg equilibrium for most of the loci, with only two loci not being at the equilibrium in all populations. No linkage disequilibrium was detected among all pairs of loci tested. These new markers will be a useful tool to study the intra- and interspecific genetic structure of these African agricultural pests and will help disentangling their well-known classification issues.