Mangrove forests are distributed in the intertidal zones of tropical and subtropical regions, and have been severely damaged by anthropogenic activities, climate change, and stochastic events. Although much progress has been made in the conservation and restoration of mangroves in China, studies of the genetic diversity of mangroves are lacking, especially for isolated populations, yet such studies are essential for guiding conservation and restoration efforts. Here, we evaluated the genetic diversity, spatial genetic structure, and mating system of two mangrove species, Rhizophora apiculata and Avicennia marina, in a heavily disturbed area in Tielu Harbor, Sanya City, Hainan Island, China, using 18 nuclear microsatellite markers. We found that the genetic diversity of R. apiculata, which is classified as ‘Vulnerable’ in the China Red List categories, was high and similar compared with the genetic diversity estimates of other populations reported in previous studies. In contrast, the genetic diversity of A. marina, which is classified as a species of ‘Least Concern’, was low compared with the genetic diversity estimates of other populations. We then evaluated the presence of genetic bottlenecks, spatial genetic structure, and the mating system to determine the effects that habitat destruction has had on these two species. Our findings indicate that distinct conservation and restoration approaches are needed for these two species. Generally, our results provide valuable information that will aid the development of conservation and restoration strategies for the mangroves of Tielu Harbor.