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Although the genus Cordylus has received much recent attention, previous studies have failed to include all known species, particularly for biogeographically important taxa. Recent fieldwork targeted a previously known population of Cordylus rivae from the southeast of Ethiopia’s Oromia region and we consequently found two individuals of this poorly documented species. We then sequenced 3 102 base pairs from both mitochondrial (12S, 16S) and nuclear (Kif24, MC1r, MYH, PRLR) gene regions for these individuals-the first ever genomic material for this taxon-and compared these data with those previously published for other Cordylus species. We analyzed these data using both phylogenetically relevant optimality criteria (i.e. Maximum Likelihood and Bayesian inference) as well as distance-based methods. Cordylus rivae forms a unique clade and groups closely with the other members of the East African Cordylus, particularly C. beraducci-the closest geographic neighbour. We discuss the biogeographic and conservation implications of C. rivae’s current distribution and make some suggestions concerning future research into this poorly known species.