Carpentaria acuminata occurs in monsoon rainforest and is endemic to the Northern Territory, Australia. The genetic diversity of C. acuminata populations was surveyed across the geographical range of the species using isozyme analysis. Genetic diversity within C. acuminata populations (HE = 0.143) was typical of rainforest species and woody angiosperms generally. Genetic diversity was not correlated with rainforest patch size. However, there was significant heterogeneity among populations (FST = 0.379), with infrequent effective gene flow among populations (Nm = 0.39). Genetic diversity was negatively correlated with increasing distance between neighbouring C. acuminata populations, but geographical distance was not a good predictor of genetic similarity. C. acuminata is a favoured food of mobile frugivores such as Torres Strait pigeons and flying foxes. The decreased diversity with decreasing density of populations indicated that seed dispersal by frugivores has been important for the maintenance of diversity in this species. Populations known to have originated on relatively young, Holocene landforms were not necessarily genetically depauperate. Gene flow by pollen is apparently limited because C. acuminata populations are significantly inbred regardless of genetic diversity (F = 0.641). The distribution and diversity of rare alleles, i.e. those occurring in few populations, is consistent with the theory of rainforest contraction during the Pleistocene.