The spiral-horned antelopes (genus Tragelaphus) are among the most phenotypically diverse of all large mammals, and evolved in Africa during an adaptive radiation that began in the late Miocene, around 6 million years ago. Tragelaphus was able to exploit the habitat heterogeneity created by Plio-Pleistocene paleoclimatic fluctuations and tectonic processes to eventually occupy almost every habitat type in present day sub-Saharan Africa. The smallest of the spiral-horned antelopes, the bushbuck (T. scriptus), is also widely distributed across Africa, but is genetically divided into polyphyletic Scriptus and Sylvaticus mitochondrial (mt)DNA superlineages that inhabit opposite halves of the continent, suggesting the convergent evolution of independent bushbuck species. In this study, we provide a species tree reconstruction for the genus Tragelaphus and show that Scriptus and Sylvaticus are reciprocally monophyletic at nuclear DNA loci, comprising a single species across its African range. Given that mtDNA will sort into species-specific lineages more quickly than nuclear DNA, only an ancient interspecific hybridization event between a female from a now-extinct Tragelaphus species and a proto-Scriptus bushbuck male can reconcile the mito-nuclear incongruence. This extinct species diverged from the nyala (T. angasii) in the Pliocene about 4.1 million years ago. This study adds to an increasing body of evidence that suggests interspecific hybridization may be more common than previously thought.