AbstractMicrosatellite variation from eight loci was studied in five populations of Drosophila teissieri, a fruit‐fly found only in the rain forests of sub‐Saharan Africa. Five noncontiguous rain forest sites (from Tanzania, Gabon and Ivory Coast) were sampled to measure the effects of historical forest fragmentation on population structure in an obligatory forest‐dwelling species. The Ivory Coast and Gabon populations showed a wider range of alleles, different modal alleles and had a higher genetic diversity than the three East African populations. As could be expected, genetic differentiation (FST) was significantly correlated with physical distance, but the westernmost population (Ivory Coast) showed values that were intermediate between the central (Gabon) and Eastern (Tanzania) populations. A migration‐drift equilibrium in a stable continuum of populations did not appear adequate to describe the observed distribution. It seems probable that the species has undergone abrupt changes involving isolation, merging and migration of populations, as a consequence of repeated waves of forest fragmentation and coalescence.