In this issue of Molecular Ecology, Gueguen et al. (2010) describe their novel approach to resolving cryptic genetic diversity in the Bemisia tabaci complex (Hemiptera: Aleyrodidae.) Complexes of cryptic species present a challenge to both morphological and molecular taxonomy – the former presumed, as shared morphology normally defines species as cryptic, but the latter also problematic when host DNA sequence data is either inconclusive or unaccompanied by independent evidence. Endosymbiont associations with insect hosts have, historically, complicated efforts to develop a robust molecular taxonomy, but the approach of Gueguen et al. takes advantage of endosymbiont community composition to help rather than hinder the task of resolving taxonomic distinctions within the B. tabaci complex.