We analyzed the genetic diversity and structure of three allopatric populations of the Pacific red snapper Lutjanus peru (Nichols and Murphy, 1922) by means of restriction fragment length polymorphisms of the entire mitochondrial control region (1350 bp). We found high levels of haplotype (h = 0.966) and nucleotide (π = 3.23%) diversities among the 100 organisms analyzed from Baja California Sur, Sinaloa and Jalisco (Mexico). Most of the molecular variability was detected with only one of the five restriction enzymes used (MseI). Heterogeneity analysis of haplotype frequencies was not significant (χ2 = 125.1, P > 0.25); neither were Wright's fixation index (FST = 0.0062, P = 0.140) nor its molecular analogue (ΦST = 0.0194, P = 0.056). An analysis of molecular variance (AMOVA) confirmed the absence of differentiation between peninsular and continental populations, even though it produced a marginally significant ΦST (ΦST = 0.0116, P = 0.048). No phylogeographic pattern was detected in a Neighbor-Joining gene tree. We argue that high molecular diversity levels are consistent with a large population size and that the absence of an apparent genetic structure, in the extreme north of the species distribution, suggests the action of mechanisms favoring passive larval transport among allopatric populations; although active adult migration cannot be ruled out.