<p>Mitochondrial DNA (mtDNA) barcoding has transformed the study of mammalian diversity, particularly in bats, by providing a cost-effective and widely accessible method for rapid, non-invasive species identification. Its utility stems from the ease of amplification, even from degraded material such as faeces, and the extensive availability of reference sequences in public databases. However, reliance on mtDNA alone risks misinterpretation of species boundaries, as numerous studies now demonstrate widespread mito-nuclear discordance and introgression across bat taxa in Europe, Asia, Africa, and the Americas. In some taxa, introgression has resulted in complete mitochondrial replacement, whereas in others it is geographically restricted to contact zones. These patterns highlight the evolutionary lability of bat mitochondrial genomes and emphasise the need to integrate nuclear markers, particularly when studying hybrid zones or poorly surveyed regions. Although mtDNA remains invaluable for preliminary screening and large-scale biodiversity assessments, the growing body of evidence cautions against its exclusive use for taxonomic inference or conservation decisions, especially when based on minimal sampling or weak auxiliary evidence. Incorporating nuclear data, including from non-invasive samples, will be essential for accurately delineating species boundaries and advancing our understanding of their evolutionary history. Furthermore, integrating complementary lines of evidence, such as acoustic, morphological, behavioural, and ecological data, should be prioritised to achieve a more comprehensive understanding of species diversity.</p>