In this study, tundra N2O and CH4 fluxes were measured from one seabird sanctuary (SBT) and two non-seabird colonies (NST-I and NST-II) in Ny-Ålesund (79°55′N, 11°56′E), Svalbard during the summers of 2008 and 2009. N2O and CH4 fluxes from SBT showed large temporal and spatial variations depending on the intensity of seabird activity. High seabird activity sites showed large N2O and CH4 emissions while low N2O and CH4 emissions, even CH4 uptake occurred at medium and low seabird activity sites. Overall the mean fluxes were 18.3 ± 3.6 μg N2O m−2 h−1 and 53.5 ± 20.3 μg CH4 m−2 h−1 from tundra SBT whereas tundra NST-I and NST-II represented a relatively weak N2O source (8.3 ± 13.2 μg N2O m−2 h−1) and strong CH4 sink (−82.8 ± 22.3 μg CH4 m−2 h−1). Seabird activity was the strongest control of N2O and CH4 fluxes compared with soil temperature and moisture, and high N2O and CH4 emissions were created by soil physical and chemical processes (the sufficient supply of nutrients NH4+–N, NO3−–N, total nitrogen, total phosphorus and total carbon from seabird guano, seabird tramp and appropriate water content) related to the seabird activity. Our work suggests that tundra ecosystems impacted by seabird activity are the potential “hotspots” for N2O and CH4 emissions although these sources have been largely neglected at present. Furthermore the combination of seabird activity and warming climate will likely further enhance N2O and CH4 emissions from the High Arctic tundra.