Parasite population structure can be used to infer fine-scale movement in host species. Many penguin species form large social colonies, and are highly philopatric, returning to the same nest or burrow, along the same route, after each trip to sea. Within a colony, however, the local abundance, physical similarity, and nocturnal habits of penguins hinder the observation of fine-scale movements. To determine the extent of movement and interaction of penguins within colonies, a genotyping by sequencing (GBS) approach was used to study the fine-scale structure of ticks—which depend on host movements for dispersal—exploiting the largest Little Penguin (Eudyptula novaehollandiae) colony in Australia (Phillip Island, Victoria). No barriers to tick gene flow were identified, and we infer that extensive penguin movement occurs throughout the colony. Our findings support the hypothesis that some penguin species are highly gregarious, socializing widely within colonies despite strong nest-site philopatry.