BACKGROUND The taxonomy of the species complex Bemisia tabaci, a serious agricultural pest worldwide, is not well resolved yet, even though species delimitation is critical for designing effective control strategies. Based on a threshold of 3.5% mitochondrial (mtCOI) sequence divergence, recent studies have identified 28 putative species. Among them, mitochondrial variability associated with particular symbiotic compositions (=cytotypes) can be observed, as in MED, which raises the question of whether it is a single or a complex of biological species. RESULTS Using microsatellites, an investigation was made of the genetic relatedness of Q1 and ASL cytotypes that belong to MED. Samples of the two cytotypes were collected in West Africa where they live in sympatry on the same hosts. Genotyping revealed a high level of differentiation, without evidence of gene flow. Moreover, they differed highly in frequencies of resistance alleles to insecticides, which were much higher in Q1 than in ASL. CONCLUSION Q1 and ASL are sufficiently reproductively isolated for the introgression of neutral alleles to be prevented, suggesting that they are actually different species. This indicates that nuclear genetic differentiation must be investigated within groups with less than 3.5% mtCOI divergence in order to elucidate the taxonomy of B. tabaci at a finer level. Overall, these data provide important information for pest management.