The aim of this study was to investigate the mating system and genetic diversity of the palm Copernicia prunifera using inter-simple sequence repeat markers. We found that the C. prunifera has multiple inflorescences with hermaphroditic flowers and pollen viability of 62%. Outcrossing rates at the population level (N = 267) produced a multilocus outcrossing rate (tm) of 0.878 and a single-locus outcrossing rate (ts) of 0.738, indicating that C. prunifera has a mixed mating system that is preferentially allogamous. The rate of mating among relatives (tm - ts) was low, indicating limited outcrossing between closely related individuals. The fixation index between seed trees (F) was negative (-0.200), suggesting an absence of inbreeding, while the correlation of selfing (rs) was high (0.914). The values of the diversity indices among adults and progenies did not differ statistically (HE = 0.319 and I = 0.470; HE = 0.337 and I = 0.505, respectively). In testing for the presence of genetic bottlenecks using the infinite allele model and the stepwise mutation model, we observed a reduction in the effective population, as well as a deficit in heterozygosity (P <0.0001). The results of this study inform management strategies for the conservation and genetic improvement of the C. prunifera palm.