Anthropogenic impacts contribute to the fragmentation of urban mangrove forests, and in the Sydney region of Australia, Avicennia marina is commonly found in small stands of <50 adult trees that have altered pollinator services. However, genetic diversity may not vary with stand size because insufficient time has passed since stands were established or pollen and propagule dispersal are sufficient to overwhelm the effects of genetic drift and founder events. We tested the predictions that, despite the potential of mangroves for dispersal of propagules by water and long distance dispersal of pollen by honeybees, fragmentation and localized foraging by honeybees causes small stands of A. marina to display reduced genetic diversity and elevated inbreeding. Using four microsatellite markers, we quantified the genetic and genotypic diversity present within samples of 20 adults taken from three large (>1500 trees), intermediate (300–500 trees) and small (<50 trees) stands within each of two urbanized estuaries and estimated mating system parameters using progeny arrays for sets of five adults within the large and small stands. We detected no significant effect of stand size on levels of single-locus genetic diversity. There were low, although significant, levels of allelic differentiation within (F SE = 0.021, P = 0.003) and among (F ET = 0.055, P = 0.005) estuaries but no evidence of isolation by distance. In contrast, our analysis of progeny arrays revealed that, while all stands displayed high levels of biparental inbreeding, an expected consequence of pollination by honeybees, current outcrossing rates (t m ) were significantly lower in small (0.55) as compared to large (0.75) stands. The genetic makeup of the adult populations imply that stands are interconnected and suggest little impact of habitat fragmentation, while the progeny arrays suggest that plants within small stands may display reduced fitness.