Damping-off and stem rot of cowpea caused by Sclerotium rolfsii has previously been reported in Benin, where the pathogen showed variation in growth and sclerotia production among isolates. Pathogenicity, mycelial compatibility group (MCG) tests and rDNA sequence analyses were conducted on different isolates of S. rolfsii and S. delphinii collected from different hosts and geographical areas in Benin and South Africa. All the isolates, when inoculated into soil and planted with cowpea, caused damping-off and stem rot symptoms. Aggressiveness among isolates varied depending on the host from which each was isolated. Isolates originating from cowpea produced the highest disease incidence followed by isolates from peanuts. Four MCGs were distinguished among 66 isolates. Isolates from the same hosts tended to group into the same MCG. The incidence of damping-off and stem rot of cowpea, expressed as percentage diseased plants, varied among MCGs. Plants inoculated with MCG2 displayed the highest disease incidence, whereas MCG4 resulted in the least. Parsimony analysis of ITS DNA sequence data supported a close affinity of the Sclerotium spp. but showed genetic variation among isolates with no grouping based on host of origin.