Uncovering the genomic landscape of divergence in taxa with “porous” species boundaries is of great interest in evolutionary and ecological biology. With the advances of next generation sequencing (NGS), many thousands of single nucleotide polymorphisms (SNPs) can be genotyped for hundreds of individuals in divergent species within reasonable time and budget. This makes the studies of genome-wide divergence feasible in non-model organisms. We investigated the genomic divergence and introgression between Rhizophora mucronata and R. stylosa, two sympatric mangrove species with detectable ecological divergence and minor morphological differences, using restriction site associated DNA (RAD) sequencing. The reduced genomes of 94 individuals from six populations in three sympatric sites of R. mucronata and R. stylosa were sequenced using Illumina HiSeq 4000. The short reads were mapped to R. apiculata scaffold genome and >42 000 SNPs were discovered. The overall genomic differentiation between R. mucronata and R. stylosa was substantial in SE Asia, with high FST at many genomic regions. In contrast, the relative low genomic divergence between sympatric populations in Australia may indicate a lack of reproductive isolation and introgression between the two close-related taxa, or various degree of admixture in ancestry among the individuals at the site. We also detected extensive heterogeneity along the genome in divergence between R. mucronata and R. stylosa, as some extremely high FST as well as a few very lows were detected in some genomic regions, which could result from divergent or convergent selection at different loci in the genome.