We assayed genetic variations at five microsatellite loci of dolphinfish captured at five sites in 2005 and eight sites in 2006 to detect genetic population structure of dolphinfish Coryphaena hippurus in the Gulf of California and surrounding waters. Results show high genetic variation, similar to other pelagic fishes with large populations. Pairwise FST values and hierarchical AMOVA detected subtle but significant spatial and temporal heterogeneity, mainly in samples of 2005 and some of 2006. However, Bayesian assignment analysis failed to detect genetic differentiation, which was also supported by the Mantel test and gene flow estimates among the sampled sites. This suggests that, despite the slight heterogeneity detected in this region, the dolphinfish forms a single panmictic population with high genetic variation and gene flow. © 2010 Elsevier B.V.