Mangroves consist of a group of taxonomically diverse species representing about 20 families of angiosperms. However, little is known about their reproductive biology, genetic structure, and the ecological and genetic factors affecting this structure. Comparative studies of various mangrove species are needed to fill such gaps in our knowledge. The pollination biology, outcrossing rate, and genetic diversity of Aegiceras corniculatum were investigated in this study. Pollination experiments suggested that the species is predominantly pollinator-dependent in fruit setting. A quantitative analysis of the mating system was performed using progeny arrays assayed for intersimple sequence repeat (ISSR) markers. The multilocus outcrossing rate (tm) was estimated to be 0.653 in a wild population. Both allozyme and ISSR were used to investigate genetic variation within and among populations. The combined effects of founder events and enhanced local gene flow through seedling dispersal by ocean currents apparently played an important role in shaping the population genetic structure in this mangrove species. Both allozyme variation (P = 4.76%, A = 1.05, HE = 0.024) and ISSR diversity (P = 16.18%, A = 1.061, HE = 0.039) were very low at the species level, in comparison with other woody plants with mixed-mating or outcrossing systems. Gene differentiation among populations was also low: allozyme GST = 0.106 and ISSR GST = 0.178. The unusually high genetic identities (0.997 for allozyme and 0.992 for ISSR loci), however, suggest that these populations are probably all descended from a common ancestral population with low polymorphism.