Analyses of mitochondrial and nuclear DNA sequences hitherto failed to resolve the three morphospecies of the so-called Ceratitis “FAR complex” (C. fasciventris, C. anonae, C. rosa). Therefore, we developed a set of microsatellite markers for a first population genetic survey of this species complex. Specimens of C. fasciventris, C. anonae, and C. rosa (27 populations, n=621) collected across their respective distribution ranges were genotyped at 16 polymorphic microsats. Genetic distance analyses distinguished at least five bootstrap supported population groups, each including samples from one of the three morphospecies. The Bayesian assignments implemented in STRUCTURE show that (1) C. rosa is represented by at least two clusters of individuals (R1, R2) that can occur in sympatry/parapatry, but that may have different developmental thresholds, (2) C. fasciventris is represented by at least two, geographically separated, clusters (F1, F2), and (3) C. anonae is genetically more homogeneous and doesn’t show a clear intraspecific structuring (cluster A). The differentiation of the C. rosa and C. fasciventris clusters is supported by morphological differences in the male secondary sexual characters. Genetic divergences between the C. rosa clusters and between the C. fasciventris clusters are comparable to the interspecific divergences among C. fasciventris, C. anonae, and C. rosa. Higher genetic distances were observed between the morphologically similar C. rosa and C. fasciventris, while C. anonae appears as closely related to both F1 and R2. The microsats used in this study thus unmasked a complex, and partly cryptic, population genetic structure within the FAR morphospecies. Keywords: Tephritidae, population genetics, microsats

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