Seabirds play an important role as top consumers in the food web and can be used as biomonitors for exposure to pollutants. Erythrocyte nuclear abnormalities (ENAs) represent one of the most important ways to detect genomic damage associated with environmental degradation and pollution. This study investigates the number of ENAs in three populations of two species of Leucocarbo shags. Blood samples from the Antarctic shag (Leucocarbo bransfieldensis) breeding on the Antarctic Peninsula and the South Shetland Islands and the South Georgia shag (Leucocarbo georgianus) breeding on the South Orkney Islands were analysed. The results revealed evidence of genomic damage in all individuals, with a mean number of ENAs of 26.54 and 43.51/10 000 red blood cells for Antarctic and South Georgia shags, respectively. Thus, the shags from the Orkney Islands showed a higher number of erythrocyte abnormalities, whereas no significant differences were observed among shag populations across the Antarctic Peninsula and South Shetland Islands. These results suggest that, in the northern part of the region, shags might be more exposed to pollutants. They also provide the first reference values for cytogenetic damage in this species and establish a critical baseline for future biomonitoring efforts.