The dynamics of methane (CH4) flux in relation to populations of methanogenic and methanotrophic bacteria was studied under the different biophysical conditions of the Indian Sundarban mangrove ecosystem. Soil depth profile analysis (up to 60 cm) in the lower littoral zone (LLZ) revealed that a methanogenic population of 6.45 ± 0.19 × 104 cells/g dry weight (dry wt) of soil accounted for a CH4 production rate of 6.23 ± 3.53 × 103 µmol m−2 day−1, whereas in the surface soil, a methanogenic population of 3.34 ± 0.37 × 104cells/g dry wt of soil accounted for a CH4production rate of 31.6 ± 0.57 µmol m−2 day−1. The CH4oxidation rate at 60 cm depth in the LLZ was 24.42 ± 1.28 µmol m−2 day−1, with an average methanotrophic population of 1.33 ± 0.43 × 104cells/g dry wt of soil, whereas in the surface soil, the oxidation rate and average population were 3.38 ± 1.43 × 103µmol m−2 day−1and 12.80 ± 2.54 × 104cells/g dry wt of soil, respectively. A similar soil profile in terms of CH4dynamics and the populations of methanogenic and methanotrophic bacteria was found in the mid-littoral and upper littoral zones of the studied area. The results demonstrate that most of the produced CH4(approximately 60%) was oxidized by methanotrophic bacteria present in the soil, thus revealing their principal role in regulating the CH4flux from this unique ecosystem. © 2018 Blackwell Verlag GmbH