We investigated nutrient composition and the potential for greenhouse gas production in Antarctic penguin guano, ornithogenic soils and seal colony soils through a laboratory incubation experiment. Total organic carbon contents ranged from 0.2–14.7% and total nitrogen contents ranged from 0.05–3.60% across all the samples. Penguin guano and the soils had the δ13Corg values of -28.4‰ to -22.8‰ and highly enriched δ15N values (8.28–35.51‰), indicating a rapid N cycling in local ecosystems. The mean CO2 and CH4 emission rates from penguin guano were significantly higher than those from the soils under aerobic or anaerobic conditions. The CO2-C/TOC rate indicated that the bioavailability of TOC was markedly higher in penguin guano than in the soils. These soils showed higher N2O emission rates under anaerobic conditions, indicating that denitrification may be the major process in N2O emission. The CO2 and CH4 emissions have a significant correlation with TOC in both penguin guano and the soils. Our results show that marine animal excreta are an important factor determining storage and composition of nutrients in coastal Antarctica, and that they may considerably affect current and future net fluxes of greenhouse gases in this region.