Heritiera littoralis is a mangrove species distributed in intertidal wetland and inland. Genetic variation between 6 natural populations of H. littoralis from south China was evaluated using inter-simple sequence repeats (ISSR) markers. Eleven SSR primers gave rise to 119 discernible DNA fragments of which 95 (83.19%) were polymorphic, indicating a considerable genetic variation at specific level. However, a low polymorphism at population level was detected. Both the AMOVA analysis and the dendrogram based on Nei’s genetic distances and UPGMA clustering analysis showed that there was no distinct genetic divergence between the two kinds of populations (intertidal wetland vs. inland).