The African baobab’s (Adansonia digitata) breeding system has not been experimentally verified, and it remains unclear why such a stark disparity exists between ‘male’ trees that produce few, if any, fruit, and ‘female’ trees that produce many fruit consistently year after year. Combined results from gene flow analyses of 26 trees scored for nine microsatellite loci and hand-pollination experiments on five trees across three baobab populations in Mutale District, Limpopo Province, South Africa, investigated the breeding system, strength of incompatibility within trees, and if genetic differentiation was detectable between ‘males’ and ‘females.’ Our data suggest that A. digitata is largely self-incompatible. ‘Male’ and ‘female’ trees showed high heterozygosity and estimated outcrossing rates did not differ in degree of self-incompatibility, and showed no significant genetic differentiation. The ability of ‘males’ to produce fruit if cross-pollinated suggests that poor fruit production in male trees is most likely due to low rates of pollination.
