The Antarctic Peninsula has experienced a strong climate warming trend of + 0.53 °C (mean annual air temperature) over the last 50 years. In the Polar Regions, changes in vegetation and permafrost due to a warming climate are expected to produce strong feedbacks to climate and, despite their relatively small areal extent, ice-free areas in Antarctica provide unique natural environments for studying these effects. Off the Antarctic Peninsula, close to Rothera Research Station on Adelaide Island, we used in situ measurements to assess whether spatial variation of CO2 fluxes exists a) among three important and typical vegetation types at Rothera Point during the daylight period; b) across four different ecosystem types (from Antarctic vascular tundra to barren soil) on neighbouring Anchorage Island during the peak of the growing season (January–February 2009). We aimed to assess whether Net Ecosystem Exchange (NEE), Ecosystem Respiration (ER) and Gross Ecosystem Photosynthesis (GEP) change among the selected ecosystem types and determine which environmental factors (soil moisture, soil temperature and PAR) influence NEE and ER. The data obtained at Rothera Point confirmed the presence of spatial variation of CO2 fluxes related to vegetation type, and temporal variation of the CO2 cycle during the daylight period for moss and barren soil ecosystems. At Anchorage Island the spatial variation of CO2 fluxes was mainly influenced by vegetation type at inter-community level. Deschampsia and Sanionia showed higher NEE and ER values (− 0.03 / 0.43 μmol CO2 m− 2 s− 1 for Deschampsia NEE; 0 / 0.62 μmol CO2 m− 2 s− 1Sanionia NEE; 0.27 / 2.03 μmol CO2 m− 2 s− 1Deschampsia ER; 0.31 / 1.7 μmol CO2 m− 2 s− 1Sanionia ER) than the other vegetation types studied. We measured generally positive NEE values probably due to high soil respiration. Our data suggest that ecosystems such as those studied may act as a source for CO2 release to the atmosphere and that this source effect is likely to continue and/or to increase until the “legacy” of organic matter and nutrients stored in the soils is largely decomposed.