Understanding genetic connectivity is fundamental to the design of marine protected areas in the service of ecosystem-scale management. Here we evaluate such trends for a Pacific surgeonfish (Acanthurus nigroris; N = 544) at two spatial scales: (1) within the Hawaiian archipelago, and (2) across the entire species range from the central to southwest Pacific. The mtDNA cytochrome b data reveal genetic divergence (d = 0.041) between Hawaii and the rest of the Pacific range indicating a cryptic species pair, with one taxon endemic to Hawaii. Johnston Atoll, 1400 km SW of Hawaii, also has the Hawaiian species but is distinct from most Hawaiian locations in population genetic comparisons, indicating the limits of gene flow for this widespread reef species. No consistent population genetic differences were observed among Hawaiian sites or among the other Pacific island sites. We also detected a modest bias in gene flow from the southeast towards the northwest islands of the Hawaiian Archipelago, indicating that the Papahanaumokuakea Marine National Monument may be a recipient, rather than a source of propagules to replenish reef resources.