Based on their morphological and genetic similarity, several studies have proposed that Lutjanus campechanus and Lutjanus purpureus are the same species, but there is no confirmed consensus yet. A population-based study concerning otolith shape and genetic analyses was used to evaluate if L. campechanus and L. purpureus are the same species. Samples were collected from populations in the southwestern Gulf of Mexico and the Venezuelan Caribbean. Otolith shape was evaluated by traditional and outline-based geometric morphometrics. Genetic characterization was performed by sequencing the mtDNA control region and intron 8 of the nuclear gene FASD2. The otolith shape analysis did not indicate differences between species. A nested PERMANOVA identified differences in otolith shape for the nested population factor (fishing area) in morphometrics and shape indexes (p = 0.001) and otolith contour (WLT4 anterior zone, p = 0.005 and WLT4 posterodorsal zone, p = 0.002). An AMOVA found the genetic variation between geographic regions to be 10%, while intrapopulation variation was 90%. Network analysis identified an important connection between haplotypes from different regions. A phylogenetic analysis identified a monophyletic group formed by L. campechanus and L. purpureus, suggesting insufficient evolutionary distances between them. Both otolith shape and molecular analyses identified differences, not between the L. campechanus and L. purpureus species, but among their populations, suggesting that western Atlantic red snappers are experiencing a speciation process.