Whilst the use of molecular genetic techniques is widespread in the fields of population and evolutionary biology, their application within the mammalian order Chiroptera neither reflects the species richness nor the ecological and behavioural diversity of the order. This is despite the fact that the Chiroptera are problematic to study using more direct observational techniques. Here, we standardize and synthesise the current data, assess the contribution of molecular research to the study of bat species and highlight the importance of its continued and expanded use. At an inter-population level, molecular studies have demonstrated a great diversity of population genetic structure within the order. Among populations of migratory species, genetic structure appears universally low, and hence seasonal movement is likely to be the prevailing influence. However, for sedentary species an array of factors including dispersal ability, extrinsic barriers to gene flow and historical events may determine the extent of genetic partitioning among populations. Intrinsic factors such as wing morphology or roost requirements may also influence population genetic structure in sedentary bat species, a proposal which requires further research. Molecular studies have also made important contributions towards an understanding of social organisation in bats. Evidence indicates that in many polygynous species male mating success does not translate directly into reproductive success, perhaps as a result of multiple mating by females. Estimates of relatedness within and genetic structure among colonies are, in general, very low; a finding which has important implications regarding theories concerning the formation and persistence of bat social groups. Molecular studies have provided new and important insights into the ecology of bats, and have opened up exciting and previously unexplored avenues of research. The data from these studies suggest not only a predictive framework for future studies, but also the use of genetic data in the management and conservation of bat species.