In order to evaluate the use of parasites as biological tags to identify populations of the oceanic horse mackerel, Trachurus picturatus, two samples of 100 fish each, caught off the Madeira and Canary Islands from January to June 2009, were examined for the presence of anisakids, trypanorhynchs, acanthocephalans and liver coccidians. In T. picturatus from Madeira, prevalence of the coccidian Goussia cruciata reached 82%, whereas prevalence of the nematode Anisakis sp., the acanthocephalan Rhadinorhynchus cadenati and the trypanorhynch Nybelinia lingualis were 12.0%, 8.9% and 7.0%, respectively. In samples from the Canary Islands, prevalence of G. cruciata was 8.0%, Anisakis sp. and R. cadenati reached 5.0% and 42.0% respectively, and N. lingualis was not recovered. The absence of N. lingualis and the lower prevalence of Anisakis sp. appear to be related to the smaller size of the oceanic horse mackerels examined from the Canary Islands. Although significant differences in prevalence of two parasites, G. cruciata and R. cadenati, were found between the two regions investigated (χ²=125.13, df=1, p=0.000 and χ²=40.77, df=1, p=0.000), only G. cruciata was considered useful as a biological tag for the identification of populations of T. picturatus. In order to reach sound conclusions, an expansion of the temporal and spatial sampling strategy is recommended.