The past three decades have witnessed the development of molecular tools, resulting in the successful integration of genetic methods into studies of wildlife populations. Genomic DNA can be obtained from a variety of sources including blood or tissues, but also sources which do not necessarily depend on handling or observing animals, like feces, urine, hair, or shed skin. These non-invasive samples can then be used to identify individuals, gender, and species. Genetic data can also be used to assess mating systems, hybridization, gene flow, and effective population size. Conservation biology can benefit of genetic data to define management units and to provide insights into demographic patterns. We describe some applications of genetic data in the study of European bat populations, based exclusively on non-invasive samplings. The populations of many European bat species experienced a dramatic decline in the latter half of the twentieth century, and most of them are currently considered to be vulnerable or endangered species. Many aspects of bat ecology are still unknown, and genetic data provide a powerful tool, especially regarding difficulties to catch and/or observe individuals. Based on bat feces, we investigated population genetics, effective population size and parasite prevalence in the lesser horseshoe bat (Rhinolophus hipposideros). Combined with ecotoxicological data, results provided important insights on the current exposure of this bat species to several disruptors that may have contributed to its former decline. A similar sampling strategy was applied to study hybridization between two sibling cryptic bat species: the greater mouse-eared bat (Myotis myotis) and the lesser mouse-eared bat (M. blythii). These two species often form large mixed-species groups in maternity roosts, where visual counting is impossible because the two species are morphologically almost identical. Genotyping analysis and molecular sexing were used to highlight hybridization cases between the two bat species and to assess the composition of a mixed-species group. Non-invasive sampling and molecular methods were also used in archeological samples to separate DNA mixtures and identify species present at each stratum of guano cores collected in bat roosts. Finally, we present preliminary tests realized on the Yunnan snub-nosed monkey (Rhinopithecus bieti) feces samples collected in Yunnan (China). We discuss how genetic data could help future research on the ecology and conservation of the Yunnan snub-nosed monkey and other species.