Allodapine bees provide extraordinary systems for investigating the evolution of cooperation and particularly the division of reproduction in animal societies. We present the first microsatellite primers for two native Australian species (Exoneura nigrescens and E. robusta; Hymenoptera: Apidae: Xylocopinae) which allow the accurate determination of pedigrees, reproductive skew and relatedness in colonies. Up to 55 different alleles were observed per locus.