To manage fishery resources, defining the spatial distribution of biological populations is paramount. However, identification of populations can be controversial according to the methods used. The parasitofauna of the southern hake, Merluccius australis, in the Patagonian Fjord and Channel System of southern Chile, were analysed to determine if there was more than one ecological population. Samples were collected between spring 2004 and winter 2005 in three areas of the sea channels: in Chiloé (1); north of the Strait of Magellan (2); and south of the Strait of Magellan (3). In these areas, 219 hake specimens were collected, harbouring 26,071 parasites from 25 taxa. To determine whether any parasite taxon behaved as a biological tag, its abundance and prevalence was compared given body length, sex, and seasonality of the fish samples. The parasite communities among these areas were compared using GLM on the scores of the multivariate DECORANA analysis. The following criteria were used to select the taxa studied 1) taxa with a prevalence >5%, 2) parasites that accumulated through time (body length) in the fish, and 3) variability of their abundance among sites. The greatest variability in parasite abundance in these hakes was due to fish body length and sampling area, but not to fish sex and in general, not to seasonality to distinguish fish samples among the three areas. The digenean Aporocotyle australis characterized the samples from Chiloé that represented the smallest in body size. The nematode Anisakis sp. characterized the samples from south Magallanes that were the largest specimens. Fish from north Magallanes were similar in size to those of Chiloé but with smaller length range, and a transition of parasitofauna from Chiloé and south Magallanes samples. Statistical analyses of parasite taxa with a prevalence >5% and fish of all size classes (56–85 cm) showed significant differences in the parasitofauna abundance of southern hakes from the three sites. The analysis of fish length class 66–75 cm, the first maturity size, showed no significant differences among the Magallanes sites but both were different between the Chiloé sites. The parasitofauna of taxa with a prevalence >5% were useful as biological tags to discriminate between ecological stocks in the Magallanes areas compared to individual taxa but was time-consuming. Seven endoparasites and one ectoparasite are proposed as biological tags for future monitoring of ecological stocks in Chiloé and Magallanes.