In the present study, we have extended earlier taxonomic, biochemical and experimental investigations to characterize two species of Taenia from carnivores in Kenya by use of the sequences of a variable domain (D1) of nuclear ribosomal DNA and the cytochrome c oxidase subunit 1 and NADH dehydrogenase 1 genes of mitochondrial DNA. Emphasis was placed on the characterization of Taenia madoquae from the silver-backed jackal (Canis mesomelas) and Taenia regis from the lion (Panthera leo), given the previous absence of any DNA sequence data for them, and on assessing their genetic relationships with socioeconomically important taeniids. The study showed that T. regis was genetically most closely related to T. hydatigena, and T. madoquae to T. serialis, T. multiceps or T. saginata. The present findings provide a stimulus for future work on the openUP (December 2007) systematic relationships and epidemiology of lesser-known taeniid cestodes in Africa and other continents, employing mitochondrial sequence data sets.