The African anuran genus Cardioglossa contains 19 described species, most of which are distinguished from one another by striking patterns and colors. We present a well-resolved phylogeny based on analyses of mitochondrial and nuclear loci for 18 species of Cardioglossa. This provides the basis for species-delimitation analyses and interpreting historical biogeography in the genus. Whereas much of the diversification within the genus occurred among Central African lineages during the Miocene following the origin of Cardioglossa in the latest Oligocene or earliest Miocene, most species-pairs in the genus diverged more recently during the Plio-Pleistocene. The two most geographically peripheral species—C. cyaneospila in the Albertine Rift Mountains and C. occidentalis in the Upper Guinean Forests of West Africa—both diverged from other lineages during the mid-late Miocene. Because our analyses do not support C. manengouba and C. oreas as distinct species, we recognize these geographically separate and phenotypically distinct populations as subspecies of C. oreas that diverged subsequent to the origin of Mount Manengouba during the past 1.5 million years. In contrast, we find that C. leucomystax likely represents two species found in the Lower Guinean and Congolian forests, respectively. We find recent divergences between several allopatric lineages (either species or populations) that differ in coloration and pattern, including in C. nigromaculata which varies in color across its range in Central Africa and Bioko Island. These recent divergences among allopatric lineages with distinctive coloration and pattern raise new questions about the significance of these traits in this genus for which little is known of its natural history and biology.