Metazoan parasite assemblages of Pagrus pagrus inhabiting the southwestern Atlantic were analysed with the aim of identifying the existence of different stocks and to comparatively assess the value of different parasite guilds as indicators of zoogeographical regions. A total of 186 fish was examined. Samples were obtained from three Brazilian and one Argentine localities, distributed in three different biogeographic districts of the Argentine Zoogeographical Province. Pagrus pagrus harboured 26 metazoan parasite species distributed in three guilds, ectoparasites (10 species), long-lived larval endoparasites and short-lived gastrointestinal endoparasites (eight species each). Prevalence and abundance values of the former two guilds allowed analysing them comparatively to assess their value as biological indicators of both host population structure and zoogeography. Results of analyses on long-lived parasites evidenced the existence of three stocks, one in the regions of Rio de Janeiro and Sao Paulo, other in southern Brazil (Rio Grande do Sul) and a third in northern Argentina (Mar del Plata), responding to the differential environmental conditions characteristic of three zoogeographical ecoregions. Ectoparasite assemblages exhibited significant differences between all pairs of samples, including those considered as a single stock according to data on persistent parasites. Assemblages of long-lived larval parasites are considered as better indicators for stock assessment purposes than ectoparasites, whose population parameters were variable temporally and heterogeneous at small spatial scales. The distributional variability of persistent parasites of P. pagrus along large scales provides valuable information to help defining robust biogeographical patterns, applicable to stock identification and fishery management of this species.