The Pacific thread herring, Opisthonema libertate, is a fishery resource in the eastern tropical Pacific, yet its population dynamics are poorly understood. The aims of this work were to document the metazoan parasite species in O. libertate from the Gulf of California in Mexico, determine latitudinal changes in their infection levels, and assess their potential as biological tags. Six parasitic species were identified: Myosaccium ecaude and Parahemiurus merus digeneans, Cribromazocraes cf. travassosi and Mazocraeoides georgei monogeneans, Pseudoterranova sp. nematodes, and Lepeophtheirus sp. copepods. The monogenean and copepod species are reported for the first time in O. libertate. Many fish were infected with digeneans, and there was a rare occurrence of other parasites. While the prevalence and median intensity of M. ecaude and P. merus significantly varied among sampling localities, a multivariate analysis revealed a distinct separation between some localities; these results suggest that individual fish form several discrete populations. However, the utility of these parasites as biological tags will be further probed because they cannot satisfy all requirements for good biological tags. The present results might be helpful in complementing other techniques to determine the movement and stock structure of O. libertate, albeit with certain limitations.