Dolichopodidae (over 6000 described species in more than 200 genera) is one of the most speciose families of Diptera. Males of many dolichopodid species, including Dolichopus, feature conspicuous ornaments (Male Secondary Sexual Characters) that are used during courtship. Next to these MSSCs, every identification key to Dolichopus primarily uses colour characters (postocular bristles; femora) of unknown phylogenetic relevance. The phylogeny of Dolichopodidae has rarely been investigated, especially at the species level, and molecular data were hardly ever involved. We inferred phylogenetic relationships among 45 species (57 samples) of the subfamily Dolichopodinae on the basis of 32 morphological and 1415 nucleotide characters (810 for COI, 605 for Cyt-b). The monophyly of Dolichopus and Gymnoptermus as well as the separate systematic position of Ethiromyia chalybea were supported in all analyses, confirming recent findings by other authors based purely on morphology. Within Dolichopus, stable species groups could be assigned to four distinct categories on the basis of their statistical support in 7 phylogenetic analyses: (i) clades significantly supported in all analyses, (ii) clades supported in trees based on DNA and combined data, but only partly in morphological trees, (iii) clades significantly supported in trees based on DNA and combined data, but not in morphological trees, and (iv) clades consistently supported only in morphological trees. The phylogeny generated here provides a better understanding of the phylogenetic relevance of some debated morphological characters used for species and species-group characterizations in the most commonly used idenlification keys. In this respect, postocular bristle colour proved of little phylogenetic relevance since every group with species featuring black bristles also included species with partly yellow bristles. Entirely or partly infuscated femora explained the nodes of three stable species groups and even revealed an incorrect polarity of this morphological character in three species. Four of 6 complex MSSCs and 5 of 8 more common MSSCs were found consistently in further species groups.