While many studies have investigated connectivity and subdivision in marine fish occupying tropical, shallow water reef habitats, relatively few have been conducted on commercially important deep-water species in the Indo-Pacific region. Here, we examine spatial and temporal genetic variation in the deep-water oblique-banded snapper Pristipomoides zonatus, collected from eight locations across the Indian and Pacific Oceans. A total of 292 individuals were screened for genetic variation at six nuclear microsatellite loci and the cytochrome c oxidase subunit 1 (COI) mitochondrial DNA (mtDNA) gene. There was evidence of low, but significant genetic differentiation between ocean basins (FCT = 0.009) and no significant divergences between sites within oceans. The lack of population structure within ocean basins suggests P. zonatus has a long pelagic larval duration with high levels of connectivity between populations over large geographical distances (>2000 km). There was no evidence of temporal variation in allele frequencies within populations. However, ephemeral genetic divergences between sites were detected, along with a significant reduction in genetic diversity at one site, suggesting there may be low effective population sizes (Ne). Our results suggest that localized declines in genetic diversity could be offset by gene flow from other locations within ocean basins, though predicting the broader impacts of localized stock depletions requires further understanding of recruitment dynamics and life history characteristics of the species.