ABSTRACT: Restriction fragment length polymorphism analysis was performed on polymerase chain reaction-amplified DNA fragments containing the D-loop, ND2, and CO I genes of fiddler crab Uca arcuata mitochondrial DNA. In total, 316 individuals from six populations in Japan and two populations in Taiwan were analyzed using five restriction endonucleases (AfaI, BcnI, Cfr13I, HaeIII and HinfI), yielding 85 haplotypes. Samples were taken from Nakagusuku Bay, Okinawajima Island, which is the only known distribution of U. arcuata in the Ryukyu Archipelago. The Okinawajima Island population is isolated geographically from others and showed a marked low genetic variability (h = 0.2539, π = 0.0005) and significant differentiation from other population samples in haplotype composition. We suggest that a substantial decrease in the genetic variability of the Okinawajima Island population was caused by genetic drift under the conditions of small population size and low gene flow from other populations. It is important to conserve the intertidal zone in Nakagusuku Bay for the maintenance of this endangered population.