Abstract: A total of 1351 species from 63 families (759 species from the Pirin Mts. and 1003 species from the Rila Mts.) have been recorded from the two mountains so far. The low degree of similarity (46.2%) of the fauna between these mountains is related to their natural features and insufficient research. The greatest number of species has been found in the zone of the beech forests (409 species or 55.1% from Pirin Mts. and 736 species or 73.4% from the Rila Mts.). The degree of similarity between the dipteran fauna of the different vegetation belts of the two mountains ranges from 0% to 46.6%. The dipterans belong to 92 areographical categories, divided into two supergroups: 1) species with Mediterranean type of distribution: more thermophilic and distributed mainly in the southern parts of the Palaearctic (49 species or 6.5% from Pirin Mts. and 48 species or 4.8% from the Rila Mts.); 2) species with Palaearctic and Eurosiberian type of distribution: more eurybiontic and widely distributed in the Palaearctic (710 species or 93.5% from Pirin Mts. and 955 species or 95.2% from the Rila Mts.). The Holomediterranean and Mediterranean-Central Asian forms (from 0.6% to 1.3%) are the best represented in the first group. The European, Holarctic, Holoeurosiberian and Transpalaearctic taxa (from 7.8% to 19.0%) prevail in the second group. A total of 12–13 species (from 1.2% to 1.7%) are endemics. The distribution of the zoogeographical categories in the separate vegetation belts of the mountains is scrutinised.