Coral reefs, seagrass beds, and mangrove forests possess abundant fauna and form the coastal landscape in tropical and subtropical zones. These ecosystems have also been subjected to anthropogenic disturbances. Population genetics using genetic markers are useful to estimate genetic differentiation. If populations are genetically diverged by geographic and oceanographic factors, the differentiation will accumulate and form the genetic structure. Biological features such as reproductive mode also influence genetic differentiation among populations. In reef-building corals, compared to brooding species, broadcast-spawning species indicates lower genetic differentiation among populations. Furthermore, other historical factors might influence the genetic differentiation. Here, we review the genetic differentiation pattern for understanding the maintenance system of reef-building coral, seagrass, and mangrove species and is helpful for the conservation of these coastal ecosystems.
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