The bee-killing flies, genus Melaloncha, are parasitoids of bees of the family Apidae, including stingless bees, bumble bees, and the western honey bee, Apis mellifera L. With >160 described species, Melaloncha is among the largest genera in the family Phoridae. Most species are known only from females as the males typically show too few differences to be useful in characterizing species. The monophyly of Melaloncha and its two subgenera (Udamochiras and Melaloncha s.s.) is strongly supported by morphological characters, but the phylogenetic relationships among the various species and species groups are not well understood. Here, we report on a preliminary molecular phylogenetic study of 30 exemplar Melaloncha species representing both subgenera and seven species groups by using a combination of nuclear (28S and CAD) and mitochondrial (12S, 16S, ND1, and CO1) genes for a total of 3,306 bp. Maximum parsimony analysis suggested the following relationships: 1) Melaloncha is monophyletic, 2) the subgenus M. (Udamochiras) is monophyletic and is a sister-group to M. (Melaloncha), and 3) each of the species groups for which we had multiple species were monophyletic with the M. furcata-group being the sister-group to all other Group II taxa. These results support hypotheses of relationships based on morphological characters. The utility of the molecular data for associating morphologically dissimilar males and females is discussed.