We examined the systematics of two frequently confused Albertine Rift endemic treefrogs, Leptopelis karissimbensis and Leptopelis kivuensis. One mitochondrial (16S) and one nuclear (BDNF) gene were sequenced to demonstrate genetic differences between the two species. Although we did not find morphometric differences between the two taxa, several characters can be used to diagnose each species, including coloration (adult male throat), ventral pigmentation, presence/absence of a slight heel spur in large individuals, and male advertisement calls. The geographic distribution of each species is revised based on our new locality records and reconsideration of historical records from the literature. We recommend that L. karissimbensis be downgraded in conservation status to near threatened, because it does not meet the IUCN restricted geographic distribution criteria of an endangered species.