Tube-dwelling invertebrates affect microbial processes by feeding on sediment bacteria, by creating structures with properties different from that of the bulk sediment, by disturbing the benthic boundary layer, and by pumping water through their tubes. We studied the effects of Chironomidae in a flooded soil. Tubes were at least 1.5 cm long and ca. 2 mm in diameter, and extended through the anoxic subsurface soil over most of their length. Larvae had no effect on CH4 flux across the sediment surface either by diffusion or by ebullition. In vitro, CH4 oxidation rates in tubes were significantly (P<0.05) higher than those in surface and subsurface soil. At a mixing ratio of 20 000 ppmv, average CH4 oxidation rates of tubes, surface soil, and bulk soil were 2, 0.4, and 1 μmol g dry wt.−1 h−1, respectively. The number of CH4 oxidizing bacteria determined by the most probable number (MPN) technique was higher in chironomid tubes than in the other soil compartments. CH4 production in tubes was significantly (P<0.05) higher than in the anoxic bulk soil, while no CH4 was produced in the surface soil during 240 h of incubation. We conclude that chironomid tubes are microsites with an intensified microbial activity, where CH4 production and oxidation may be tightly coupled.