The Humphead wrasse (also known as the Napoleon fish), Cheilinus undulatus, is a highly prized coral reef fish, listed on CITES Appendix II and endangered on the IUCN Red List. It is widespread across much of the Indo-Pacific region. The fish has a 4-6 week pelagic egg and larval stage, suggesting the potential for high connectivity among populations. However, its range spans important biogeographic boundaries that are associated with barriers to gene flow and deep phylogeographic structure in some marine fishes and invertebrates, raising the possibility of significant population genetic structure. We describe preliminarily the genetic structure of the Humphead wrasse across much of its range and consider the implications for effective conservation. Using mitochondrial DNA sequencing (cytochrome b and control region) coupled with microsatellite analyses, we find primarily a signal of eurymixis — i.e., low, heterogeneous population genetic differentiation across much of the species’ range (F ST analogs: <0.11 cytochrome b, <0.09 control region, <0.02 microsatellites) with the exception of modest differentiation primarily toward the peripheries (e.g., Pohnpei, Seychelles; F ST analogs: 0.03–0.24 cytochrome b, 0.05–0.24 control region, 0.03–0.22 microsatellites) — though isolation by distance is not excluded. The general dearth of structure is consistent with population expansion, following an historical bottleneck and with high contemporary gene flow. The implications are that Humphead wrasse is a metapopulation and that its conservation status depends on successful management of a sufficient but currently unknown number and distribution of populations across a multi-national network.