A comparative analysis of the parasite fauna of the southern blue whiting Micromesistius australis was carried out on 165 specimens caught around the southern cone of South America in 4 fishing zones, three from the Pacific Ocean (South to Golfo de Penas, Diego Ramirez Islands and Navarino Island) and one from the Atlantic Ocean (Malvinas Islands). The goal was to detect possible population units or migratory patterns of the southern blue whiting. Fish samples from the Pacific Ocean were collected between October and December 2006 while those from Malvinas Islands were taken in December 2007. A total of 7,621 parasite individuals were collected and determined as members of 19 nominal taxa. The parasite fauna composition was similar between fishing areas but statistical analyses revealed significant differences in absolute and relative abundances of several taxa in infracommunities. After adjusting by the effect of host body size, it was found that the fishing zone had a significant effect on variations in total abundance, taxonomic richness, diversity and composition of parasite infracommunities. Some of these variations might correspond to the different local ecological scenarios in which the southern whiting inhabit around the southern cone of South America, and indicate that southern blue whiting stay and move differentially among fishing zones. These observations allow us to conclude that southern blue whiting do not constitute an ecologically homogeneous unit across the study area.