The subgenus Homoneura Wulp, 1891 (Diptera, Lauxaniidae, Homoneurinae) is highly diverse with more than 220 species known from China, representing more than 80% of the Chinese genus Homoneura Wulp, 1891. These species were assigned into 21 species groups in studies mainly focusing on the classification and description of species. The phylogenetic relationships of each subgenus of Homoneura and the phylogenetic relationship of the species groups are still not well understood. We investigated the male morphology to provide the basis to further revise the species groups of this subgenus. In this survey, 230 species were examined and 117 morphological characters obtained, a phylogenetic analysis was conducted using the maximum parsimony analysis with TNT and WinClada. The analyses yielded 45 most parsimonious trees and one strict consensus tree. A phylogenetic hypothesis is proposed dividing the subgenus Homoneura into 12 species groups: H. (H.) nigrifacies, H. (H.) pallida, H. (H.) patella, H. (H.) beckeri, H. (H.) formosae, H. (H.) henanensis, H. (H.) nigra, H. (H.) notostigma, H. (H.) ornatifrons, and H. (H.) trispina, H. (H.) laticosta, and H. (H.) quinquenotata. This research provides valuable contributions towards a better understanding of the phylogenetic relationships within the subgenus Homoneura. However, the monophyly of the genus and subgenus was not supported.