In mangrove species the past geomorphic changes in coastal regions and reproductive systems are important factors of their distribution and genetic structure of populations. However, very little is known about the levels of genetic variation of Rhiozophora species in Southeast Asia. In this study, we surveyed levels and patterns of genetic variation as well as population structure of two sympatric mangrove species, Rhizophora apiculata and R. mucronata in Thailand, using five nuclear genes and two cpDNA regions. In all investigated DNA regions, nucleotide variation within species was low, while nucleotide divergence between the two species was considerable. The nuclear genes evolved 10 times faster than the cpDNA regions. In both R. apiculata and R. mucronata, significant positive F_IS values were found, indicating deviation from Hardy-Weinberg proportions and a deficiency of heterozygotes. In both species, we found significant genetic differentiation between populations. However, the pattern of population differentiation (F_ST) of R. apiculata differed from that of R. mucronata. Our results suggest that the two investigated species have different demographic history, even though they are sympatric and have similar reproductive systems.