Many large groupers form spawning aggregations, returning to the same spawning sites in consecutive spawning seasons. Connectivity between spawning aggregations is thus assured by larval dispersal. This study looks into the genetic structure and gene flow among spawning aggregations of a large grouper, the gulf coney Hyporthodus acanthistius, in the northern Gulf of California. First, using the mitochondrial control region and 11 microsatellites, we calculated FST metrics and conducted a Bayesian clustering analysis to determine structure among 5 spawning aggregations. Shallow genetic structure was found, separating the southernmost spawning aggregate from the remainder. Second, we used the results from the structure analysis and local water circulation patterns to delineate 3 distinct models of gene flow. The best-supported model, in which the southernmost spawning aggregate formed one group and all other spawning aggregates were nested into a second group, was the one that was consistent with water circulation during the species’ spawning season. Larval retention within a seasonal anticyclonic gyre that formed during the gulf coney’s spawning season may be responsible for the patterns found. This study highlights the importance of local oceanographic conditions in dictating the structure among spawning aggregations even at small geographic scales and contributes to informed management plans for this overexploited grouper.