Cowpea, Vigna unguiculata, is an important food legume in the tropics and subtropics. However, cowpea is a complex species with more than 10 subspecies that can hybridize and produce intermediate offspring. Partly because of the complex organization of the cowpea gene pool and the lack of adequate markers for these infraspecific units, cowpea breeders are not using the wild part of the cowpea gene pool. Here, we report the molecular characterization of 34 representative accessions with 18 polymorphic simple sequence repeat (SSR) markers from coding regions. Although the SSRs failed to separate the closest groups, i.e., subsp. alba, subsp. tenuis and the perennial groups from subsp. unguiculata, a combination of 11 SSR markers could properly identify the main cowpea subspecies. Regarding the infraspecific phylogeny of cowpea, the SSR markers confirmed the special status of the annual subsp. unguiculata versus the different perennial subspecies. They suggested that subsp. protracta is the oldest subspecies, making the origin of the species in southern Africa likely. All the taxa of hybrid origin, i.e., subsp. alba, subsp. tenuis, subsp. pubescens, and the BWA group of subsp. unguiculata, are in a single clade clearly separated from subsp. unguiculata. Although a limited number of markers were tested, considering that several hundred cowpea SSRs are available, the present work shows that SSR markers can be used for the molecular characterization of cowpea subspecies and can be very helpful for understanding the complex evolutionary history of cowpea.