Warburgia ugandensis Sprague (Canellaceae) occurs in East and Central Africa, and the species is of great medicinal importance to the local communities where it occurs. As the wild populations diminish, planted stands will in future be used as the source of medicinal products as well as germplasm. This study investigated the levels of out-crossing rates to provide knowledge for proper planning in future cultivation programmes. The mating parameters estimated using the mixed mating model software MLTR) showed the species to be predominantly out-crossing 89%) with significant levels of selfing. The multi-locus population out-crossing rate was higher than the single-locus population out-crossing rate (t(m)-t(s) = 0.023; SE = 0.010), implying that there was less likelihood of mating between relatives biparental inbreeding). Low values were also obtained for the correlation of paternity, r(p(s)) = 0.028 SE = 0.040) and correlation of selfing among family, r(s) = 0.016 SE = 0.015). For most loci, allele frequencies of pollen and ovule contributions to the progeny genotypes were significantly different P < 0.05). These results indicate that with proper sampling, the populations being established for conservation, breeding and planting purposes will be able to sustain high genetic diversity found in the wild populations.