The redbelly yellowtail fusilier, Caesio cuning, has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of regional limits to connectivity across this region. However, these have focused almost exclusively on benthic reef dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no in depth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We evaluated the genetic population structure of C. cuning using a 382bp segment of the mitochondrial control region amplified from over 620 fish sampled from 33 localities across the Philippines and Indonesia. Phylogeographic analysis showed that individuals sampled from sites in western Sumatra belong to a distinct Indian-Ocean lineage, resulting in pronounced regional structure between western Sumatra and the rest of the Coral Triangle (ΦCT = 0.4796, p \u3c 0.0043). We measured additional significant population structure between central Southeast Asia and eastern Indonesia (ΦCT = 0.0450, 36 p \u3c 0.0002). These data in conjunction with spatial analyses indicate that there are two major lineages of C. cuning and at least three distinct management units across the region. The location of genetic breaks as well as the distribution of divergent haplotypes across our sampling range suggests that current oceanographic patterns could be contributing to observed patterns of structure
