Summary Aerenchymatic transport is an important mechanism through which plants affect methane (CH4) emissions from peatlands. Controlling environmental factors and the effects of plant phenology remain, however, uncertain. We identified factors controlling seasonal CH4 flux rate and investigated transport efficiency (flux rate per unit of rhizospheric porewater CH4 concentration). We measured CH4 fluxes through individual shoots of Carex rostrata, Menyanthes trifoliata, Betula nana and Salix lapponum throughout growing seasons in 2020 and 2021 and Equisetum fluviatile and Comarum palustre in high summer 2021 along with water‐table level, peat temperature and porewater CH4 concentration. CH4 flux rate of C. rostrata was related to plant phenology and peat temperature. Flux rates of M. trifoliata and shrubs B. nana and S. lapponum were insensitive to the investigated environmental variables. In high summer, flux rate and efficiency were highest for C. rostrata (6.86 mg m−2 h−1 and 0.36 mg m−2 h−1 (μmol l−1)−1, respectively). Menyanthes trifoliata showed a high flux rate, but limited efficiency. Low flux rates and efficiency were detected for the remaining species. Knowledge of the species‐specific CH4 flux rate and their different responses to plant phenology and environmental factors can significantly improve the estimation of ecosystem‐scale CH4 dynamics in boreal peatlands.

<p>Recent studies have identified the significant role of plants in controlling methane (CH<sub>4</sub>) emission from peatlands by acting as conduits and further demonstrated that such conduit effect is species-specific. In most studies, species-specific plant-mediated CH<sub>4</sub> transport has been estimated indirectly by comparing CH<sub>4</sub> flux from surfaces with different plant communities to that from surfaces where plants responsible for CH<sub>4</sub> transport are cut, known as the clipping technique. However, the estimation based on the clipping technique has shown large uncertainty due to the plant residual effect. Thus, directly investigating the variation in CH<sub>4</sub> transport between different plant species and the factors affecting it is necessary to more precisely assess changes in the CH<sub>4</sub> fluxes of peatland ecosystems in a changing environment.</p><p>We measured CH<sub>4</sub> emission directly from shoots of <em>Carex rostrata</em>, <em>Menyanthes trifoliata</em>, <em>Betula nana</em>, and <em>Salix lapponum</em> from the early growing season until the beginning of senescence (June-September 2020 and 2021, three campaigns both years), with three specimens per species and campaign. We also measured CH<sub>4</sub> emission from <em>Equisetum fluviatile</em> and <em>Comarum palustre</em> during high summer in 2021 to further shed light on species-specific characteristics of plant-mediated CH<sub>4 </sub>flux. We monitored abiotic factors such as belowground CH<sub>4</sub> concentration, potential CH<sub>4</sub> production and oxidation rate, water table level, and peat temperature.</p><p>During high summer in 2021, <em>C. rostrata</em> had the highest CH<sub>4 </sub>transport rate per leaf area (6.86 mg m<sup>-2</sup> h<sup>-1</sup>). This value was significantly higher than that from M. trifoliata which was the secondarily important CH<sub>4</sub> emitter with the rate of 4.07 mg m<sup>-2</sup> h<sup>-1</sup>. <em>E. fluviatile</em>, <em>C. palustre</em>, <em>B. nana</em>, and <em>S. lapponum </em>had limited CH<sub>4</sub> transport rate per leaf area (0.66, 0.02, 0.14, and 0.15 mg m<sup>-2</sup> h<sup>-1</sup>, respectively) and thus were negligible CH<sub>4</sub> emitters. CH<sub>4</sub> emission from <em>C. rostrata</em> demonstrated the most pronounced seasonal variation (ranging from 0.02 to 24.78 mg m<sup>-2</sup> h<sup>-1</sup>), driven primarily by seasonal vegetation development (phenology) and only secondarily by rhizospheric peat temperature. In contrast, CH<sub>4</sub> emission from <em>M. trifoliata</em>, <em>B. nana</em>, and <em>S. lapponum</em> showed little seasonal variation, and no factors that significantly affected the flux from these species were found. Lastly, the sharp decrease in rhizospheric peat CH<sub>4</sub> concentration during high summer and the simultaneous increase in emission from <em>C. rostrata, the most dominant species in our site, </em>indicated the conduit effect predominated over the CH<sub>4</sub> production and oxidation. The findings highlight the importance of <em>C. rostrata</em> in mediating CH<sub>4</sub>, which could exacerbate the climatic impact of the thawing permafrost region where <em>C. rostrata</em> can thrive in wet microsites.</p>