Soils in the permafrost region have acted as car- bon sinks for thousands of years. As a result of global warming, permafrost soils are thawing and will potentially release greenhouse gases (GHGs) such as methane (CH4) and carbon dioxide (CO2). However, small-scale spatial heterogeneities of GHG production have been neglected in previous incubation studies. Here, we used an anaerobic incubation experiment to simulate permafrost thaw along a transect from upland Yedoma to the floodplain on Kurungnakh Island. Potential CO2 and CH4 production was measured during incubation of the active layer and permafrost soils at 4 and 20 ◦C, first for 60 d (approximate length of the growing season) and then continuing for 1 year. An assessment of methanogen abundance was performed in parallel for the first 60 d. Yedoma samples from upland and slope cores remained in a lag phase during the growing season simulation, while those located in the floodplain showed high production of CH4 (6.5 × 103 μg CH4-C g−1 C) and CO2 (6.9 × 103 μg CO2-C g−1 C) at 20 ◦C. The Yedoma samples from the permafrost layer started producing CH4 after 6 months of incubation. We conclude that landscape position is a key factor triggering CH4 production during the growing season time on Kurungnakh Island.