The genetic survey of Uca borealis of Taiwan confirmed low genetic structure among four sampled populations (FST=0.047). Greater genetic variation within species was observed compared to the other crust-aceans (H=0.139 vs. 0.073). Gene flow appeared high when estimated indirectly (Nm=5.07). The results suggest that the patterns of genetic structure of U. borealis were influenced by the interaction of local selection due to habitat differences between western and northeastern estuaries and gene flow among populations along coastal areas.