The Blue Riffle Goby, Stiphodon caeruleus (Gobiidae: Sicydiinae), is an amphidromous species endemic to the volcanic islands of Kosrae and Pohnpei, Federated States of Micronesia, in the eastern Caroline Islands. This study evaluated the population genetic structure and demographic history of S. caeruleus using mitochondrial NADH subunits 4 (ND4) and 4L (ND4L) DNA sequences. A total of 876 base pairs were successfully sequenced for 208 specimens from 15 localities. Twenty-three haplotypes were recovered with diversity indices of h  =  0.489±0.043 and π  =  0.097±0.012% that are lower than many other marine species. The median-joining network of haplotypes is star-like in formation and displayed no genetic structure. AMOVA results show that 99% of the genetic variation is found within populations, rather than between streams or islands. Mismatch distribution analysis and associated statistical tests indicate that a very recent demographic expansion has occurred for the species. Bayesian skyline plot confirms a gradual demographic expansion over the past 5000 years. This expansion is coincident with a reduction in sea level that produced coastal plains and shallow coastal waters, and human settlement of the islands. Our analyses suggest that populations of S. caeruleus among streams are historically unstructured for ND4 and ND4L haplotypes, that larvae may be presently recruited among streams of both islands, and that further nuclear DNA investigations are warranted to resolve potential genetic divergence of populations.