UNLABELLED: Intestinal helminths often cause chronic infections, which can impact health and productivity, particularly when combined with other stressors including the environmental challenges faced by polar species. Here we employed a faecal DNA amplicon-sequencing-based approach to study on the epidemiology of tapeworms (Cestoda) in gentoo penguins sampled from colonies within the Scotia Arc. Overall, 325 faecal samples were collected from gentoo penguins at 25 locations and screened for cestode sequences within a pan-eukaryote 18S DNA profile. Four different core groups of sequences were identified as frequently occurring in the dataset, which likely represent different species or groups of cestodes. The proportion of cestode DNA reads was highly variable, displaying an over-dispersed distribution. The proportion of cestode DNA correlated with differences in microbiome composition, suggesting that these infections may influence gut microbiota or vice versa, with broader consequences for penguin health and resilience. This study highlights the need for a comprehensive understanding of both direct and indirect effects of helminths on individual and population health. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-39642-w.