Ten microsatellite loci were isolated from the African ant-plant Leonardoxa africana (Fabaceae: Caesalpinioideae). They differentiate the two most divergent subspecies of this polytypic complex, L. a. africana and L. a. gracilicaulis, showing promise for the study of gene flow. In each of these two subspecies, high levels of within-population variation were observed, with a number of alleles ranging from one to 10 in ssp. africana and from one to 7 in ssp. gracilicaulis, and heterozygosity from 0 to 0.933 in ssp. africana and to 0.867 in ssp. gracilicaulis. All loci amplified successfully in the two other subspecies of L. africana.