This study examined the phylogeography of the barnacle Fistulobalanus albicostatus, which inhabits mangroves and estuarine shores in the West Pacific. Differentiation in the mitochondrial cytochrome c oxidase subunit I (COI) and 12S ribosomal RNA (12S) genes of 401 specimens of F.albicostatus was examined in samples from 16 locations in the West Pacific, ranging from Honshu to Southern China. Our results revealed that F.albicostatus comprises two major clades exhibiting a COI divergence ranging from 1.25% to 2.8%. Clade A demonstrated the widest distribution, ranging from Japan to China, and was divided into three subclades occurring in the South China Sea (A1), Okinawa (A2), and Honshu, Korea and Qingdao (A3). Clade B was determined to be endemic to Okinawa; i.e. two endemic lineages occur in this island. Thus, F.albicostatus resembles several inter-tidal species in having clades that are endemic to Okinawan waters. Nevertheless, in contrast to the rocky inter-tidal barnacles Tetraclita spp. and Chthamalus malayensis, F.albicostatus was not found to be separated into continental and oceanic populations, but instead is divided into northern and southern clades, probably because of the Yangtze River discharge, which limits gene flow between the northern and southern populations.