With unabated encroachment of human land uses on natural habitats, there is an increased imperative to catalogue biodiversity, produce accurate identifications and understand species distributions. Such knowledge helps to increase clarity and confidence in decision-making as part of environmental impact assessments. However, taxonomic ambiguities undermine this process, even in mammals that are often assumed to be adequately described. High through-put DNA sequencing technology has exceptional power to help resolve species boundaries and taxonomic issues that remain in numerous bat groups. It can be particularly helpful in speciose groups characterised by low morphological diversity, island forms and an abundance of poorly ‘anchored’ taxonomic names. We present two simpler but typical cases where high-throughput sequencing has helped overcome the technical limitations of preceding methods. Reduced representation sequencing was used to investigate reproductive isolation between two cryptic sister taxa of Taphozous over a 1000 km long zone of potential sympatry and hybridisation; and gene capture was used to evaluate the taxonomic status of the allopatric Pilbara and more northern populations of Rhinonicteris aurantia. Genome-scale reduced representation sequencing is also comparable in cost to Sanger sequencing, and can be an efficient and cost-effective addition to an integrative approach to taxonomy.