Many marine organisms are thought to have large, continuous populations with few barriers to migration and gene flow. Some fishes, however, have a terrestrial life history stage that should restrict their movement. Many species of mudskippers in the family Gobiidae (subfamily: Oxudercinae) are obligately amphibious, requiring both aquatic and terrestrial portions of their life cycle. The obligatory terrestrial phase comes with an environmental restriction to mudflat habitats during breeding, when adults build burrows in the mud to lay their eggs. Some mudskippers even spend the majority of their time out of water, and the effects of such an environmentally restricted out-of-water phase might be reflected in the population structure of the species. On the other hand, dispersal during the aquatic larval phase could connect distant breeding populations. To test this hypothesis, we examined the population structure of the Shuttles Hoppfish (Periophthalmus modestus) throughout its range in the East and South China Seas. We collected 236 individuals from ten locations across mainland China, Hainan Island, Taiwan, Okinawa and central Japan. We used a targeted capture sequencing method, RADcap, to call SNPs from 365 loci. We found that, based on observed levels of genetic variation and population structure, populations of P. modestus are connected across large areas of continuous coastal areas and across small spans of water. However, restricted long-distance dispersal across deeper water has resulted in fragmentation of populations across these geographic features. These results are consistent with the hypothesis that a limited dispersal phase significantly affects population structure in fishes.