The pollination biology, mating system, and population genetic structure of Kandelia candel were investigated. Field observations on its pollination and reproductive biology suggested that this species is pollinator dependent for fruit set, and bee activities can lead to substantial geitonogamous selfing. Quantitative analysis of the mating system parameters was performed using progeny arrays assayed for allozyme markers. Multilocus outcrossing rates (t_m) were estimated to be 0.697 ± 0.091 and 0.797 ± 0.062 in two populations. In comparison to other plant species with mixed‐mating system, the level of allozyme variation was very low in the 13 populations sampled along the coastlines of Hong Kong. At the species level, the proportion of polymorphic loci was 20%, number of alleles per locus was 1.2, and heterozygosity was 0.0362. The total gene diversity was primarily distributed within populations (H_S = 0.0339), and the coefficient of genetic differentiation among populations was low (G_ST = 0.064). This pattern of population genetic structure suggests that gene flow, primarily in the form of water‐dispersed seedlings in viviparous mangrove species, is not as limited as previously thought. However, microgeographic pattern in allele frequency at the marker loci could still be detected between the western and eastern coastal populations.