The objectives of this study were to estimate the outcrossing rate and to explain genetic consequences of the development of seed in the endocarp in a natural population of neem in Bangladesh. Cotyledons of germinated open-pollinated seeds of individual trees were analyzed by starch-gel electrophoresis to examine allozymes. Three loci with clear Mendelian segregation were used to estimate outcrossing rate. A multilocus mixed mating model was used to evaluate the mating system. The population exhibited high outcrossing rates both for multilocus (t m =0.90±0.024) and mean single-locus (t s =0.92±0.020) estimates. The difference between these two parameters (t m –t s =0±SE 0.038) was insignificant, indicating that there was no ’biparental inbreeding’ in the population. The degree of variance of the estimates of multilocus outcrossing rates decreased when two or more loci were included. In order to elucidate the significance of polycarpy a total of 471 seeds were counted out of 440 endocarps. This mechanism appears to be a possible way of avoiding inbreeding. The results indicated that the studied neem population was predominantly allogamous.