Haplochromis pharyngalis and Haplochromis petronius, two endemic cichlids from the Lake Edward system (Uganda, Democratic Republic of the Congo), are very similar in general morphology but have been reported to differ in pharyngeal jaw morphology and distribution. This study analysed 51 morphometrics and various qualitative characteristics of 48 specimens from different localities. The morphological traits of both species strongly overlap, and differences in the pharyngeal jaw morphology correspond to a geographic morphocline. We conclude that all specimens belong to one valid species, H. pharyngalis, and consider H. petronius to be a synonym.