Abstract. Pristine boreal mires are known as substantial sinks of carbon dioxide (CO2) and net emitters of methane (CH4). Natural bogs constitute a major fraction of boreal mires. However, the bog CO2 and CH4 balances are poorly known, having been largely estimated based on discrete and short term measurements by manual chambers, and seldom using the eddy-covariance (EC) technique. Eddy-covariance (EC) measurements of CO2 and CH4 exchange were conducted in the Siikaneva mire complex in southern Finland in 2011–2016. The site is a patterned bog having a moss/sedge/shrub vegetation typical of Eurasian southern Taiga, with several ponds near the EC tower. The study presents a complete series of CO2 and CH4 EC flux measurements and identifies the environmental factors controlling the ecosystem-atmosphere CO2 and CH4 exchange. A 6-year average growing season (May–September) cumulative CO2 exchange of −60 g C m−2 was observed, which partitions into mean total respiration (Re) of 167 (146–197 annually) g C m−2 and mean gross primary production (GPP) of 228 (193–257 annually) g C m−2, while the corresponding CH4 emission amounts to 7.1 (6.4...8.4) g C m−2. The contribution of October–December CO2 and CH4 fluxes to the cumulative sums was not negligible based on the measurements during one winter. GPP, Re and CH4 fluxes increased with temperature, and did not show a strong decline even after a substantial water table drawdown in 2011. Instead, GPP, Re and FCH4 became suppressed in cool, cloudy and wet conditions of 2012. May–September cumulative net ecosystem exchange (NEE) of 2013–2016 remained at about −73 g C m−2, in contrast to the hot and dry year 2011 and the wet and cool year 2012, when suboptimal weather likely degraded the net sink by 20 and 40 g C m−2, correspondingly. The cumulative growing season sums of GPP and CH4 emission showed a strong positive relationship. The EC source area was found to be comprised of 8 distinct surface types. However, footprint analyses revealed that contributions of different surface types varied only within 10–20 % with respect to wind direction and stability conditions. Consequently, no clear link between CO2 and CH4 fluxes and footprint composition was found, despite the apparent variation of fluxes with wind direction.