The black grouper Mycteroperca bonaci is a commercially important fish off the coast of Yucatan, Mexico. To investigate possible differences between parasite communities in two different environments, 60 fish were collected from two areas during 2010 and 2011 and examined for parasites. The fish were classified into two age groups, in each of which the parameters of parasitic infection - prevalence, abundance and intensity - were determined. Parasite faunas were further described at the infracommunity level. Using both univariate (PERMANOVA) and multivariate statistical methods, the values of richness, abundance, diversity and Brillouin evenness as well as the Index values of Bray-Curtis and Jaccard for similarity were calculated and compared. The results of these tests and of CAP discriminant analyses at the two sites showed the existence of two distinct parasite communities. The parasite taxa mainly responsible for the differences were the digeneans Dollfustrema sp., Prosorhynchus spp., Lepidapedoides epinepheli and Hamacreadium mutabile, and the nematode Philometra salgadoi. The potential for some of these parasites to be used as biological tags for stock identification of M. bonaci is discussed.