Temporal and spatial variability in the Arctic introduces considerable uncertainty in the estimation of the current carbon budget and Arctic ecosystem response to climate change. Few representative measurements are available for land-surface parameterization of the Arctic tundra in regional and global climate models. In this study, the eddy covariance technique was used to measure net ecosystem CO2 exchange (NEE) of Alaskan wet sedge tundra and moist tussock tundra ecosystems during the summer (i.e., 1 June to 31 August) from 1999 to 2003 in order to quantify the seasonal and spatial variability in NEE and to determine controlling factors on NEE in these tundra ecosystems. Warmer and drier conditions prevailed for the moist tussock tundra compared with that of the wet sedge tundra. Over the 5-year period, the wet sedge tundra was a sink for carbon of 46.4 to 70.0 gC m−2 season−1, while the moist tussock tundra either lost carbon of up to 60.8 gC m−2 season−1 or was in balance. The contrasting patterns of carbon balance at the two sites demonstrate that ecosystem difference can be more important in determining landscape NEE than intraseasonal and interseasonal variability due to environmental factors with respect to NEE. The wet sedge tundra showed an acclimation (e.g., over days) to temperature, while the moist tussock tundra illustrated a strong temperature dependence. Warming and drying accentuated ecosystem respiration in the moist tussock tundra, causing a net loss of carbon. Better characterization of spatial variability in NEE and associated environmental controls is required to improve current and future estimates of the Arctic terrestrial carbon balance.