Abstract. We monitored CO2 and CH4 fluxes using eddy covariance from 19 May to 27 September 2011 in a poor fen located in northern Michigan. The objectives of this paper are to: (1) quantify the flux of CH4 from a sub-boreal peatland, and (2) determine which abiotic and biotic factors were the most correlated to the flux of CH4 over the measurement period. Net daily CH4 fluxes increased from 70 mg CH4 m−2 d−1 to 220 mg CH4 m−2 d−1 from mid May to mid July. After July, CH4 losses steadily declined to approximately 50 mg CH4 m−2 d−1 in late September. During the study period, the peatland lost 17.4 g CH4 m−2. Both abiotic and biotic variables were correlated with CH4 fluxes. When the different variables were analyzed together, the preferred model included mean daily soil temperature at 20 cm, daily net ecosystem exchange (NEE) and the interaction between mean daily soil temperature at 20 cm and NEE (R2 = 0.47, p value < 0.001). The interaction was important because the relationship between daily NEE and mean daily soil temperature with CH4 flux changed when NEE was negative (CO2 uptake from the atmosphere) or positive (CO2 losses to the atmosphere). On days when daily NEE was negative, 25% of the CH4 flux could be explained by correlations with NEE, however on days when daily NEE was positive, there was no correlation between daily NEE and the CH4 flux. In contrast, daily mean soil temperature at 20 cm was poorly correlated to changes in CH4 when NEE was negative (17%), but the correlation increased to 34% when NEE was positive. The interaction between daily NEE and mean daily soil temperature at 20 cm indicates shifting environmental controls on the CH4 flux throughout the growing season.