Although necessary to promote conservation, defining evolutionary units and naming biodiversity remain a difficult task, especially in problematic species groups that experienced a dynamic biogeographic history. In this article, we undertake such task for midwife toads of the Alytes obstetricans complex by integrating recent molecular studies altogether—multilocus phylogenies and population genetic barcoding. Despite a partly unresolved phylogeny underlain by deep cyto‐nuclear discordances, nuclear and mitochondrial evidence support the validity of six genuine lineages assigned to two different species (A. obstetricans and A. almogavarii), which could be accurately mapped across most of their ranges. In particular, we demonstrate the existence for an overlooked yet genetically distinct lineage previously confounded with A. almogavarii, confined to the northern part of Huesca Province in the Spanish Central Pyrenees. We describe this micro‐endemic as the subspecies Alytes almogavarii inigoi ssp. nov., with reports on the mating call and the larvae. Conservation genetics of eight populations of this new taxon revealed two independent conservation units, separated by topographic barriers. In the wait for upcoming genomic analyses to unravel many elusive aspects of the evolution, diversity and systematics of Alytes, the present paper offers an integrative phylogeographic overview to guide future investigations and generally illustrates how multiple lines of molecular evidence can be combined to clarify the confusing taxonomy of complex species groups.