The Hkakabo Razi region located in northern Myanmar is an Important Bird Area and part of the Eastern Himalayan Biodiversity Hotspot. Within the framework of the World Heritage Convention to enlist the site under criterion (ix) and (x), we conducted a biodiversity assessment for passerine birds using DNA barcoding and other molecular markers. Of the 441 bird species recorded, we chose 16 target species for a comparative phylogeographic study. Genetic analysis was performed for a larger number of species and helped identifying misidentified species. We found phylogeographic structure in all but one of the 16 study species. In 13 species, populations from northern Myanmar were genetically distinctive and local mitochondrial lineages differed from those found in adjacent regions by 3.9–9.9% uncorrected genetic distances (cytochrome-b). Since the genetic distinctiveness of study populations will be corroborated by further differences in morphology and song as in other South-East Asian passerines, many of them will be candidates for taxonomic splits, or in case an older taxon name is not available, for the scientific description of new taxa. Considering the short time frame of our study we predict that a great part of undetected faunal diversity in the Hkakabo Razi region will be discovered.