The phylogenetic relationships of the large, diverse genus Apocephalus Coquillett are studied using seven loci (16S, COI, NDI, 28S, AK, CAD, and TPI). Both Bayesian and Maximum Likelihood methods were used to analyze the sequences. Pre-existing taxonomic relationships, based on morphology, were largely upheld, with the notable exception of the subgenus Mesophora Borgmeier being placed deep inside the genus.Therefore, Mesophora was synonymized with Apocephalus (new synonymy) and its species referred to as belonging to the Apocephalus wheeleri group. Both methods of analysis recovered similar results, providing what we consider reasonable explanations of the data, based on morphological information.