We sampled the Darwin mud volcano (MV) for meiofaunal community and trophic structure in relation to pore-water geochemistry along a 10 m transect from a seep site on the rim of the crater towards the MV slope. Pore-water profiles indicated considerable variation in upward methane (CH4) flow among sediment cores taken along the transect, with highest flux in the seep sediment core, gradually decreasing along the transect, to no CH4 flux in the core taken at a 5 m distance. Low sulphate concentrations and high levels of total alkalinity and sulphide (H2S) suggested that anaerobic oxidation of methane (AOM) occurred close to the sediment surface in the seep sediment core. High H2S levels had a genus- and species-specific impact on meiofaunal densities. Nematode genus composition varied gradually between sediment cores, with the genus Sabatieria dominating almost all sediment cores. However, genus diversity increased with increasing distance from the seep site. These limited data suggest that the community structure of seep meiofauna is highly dependent on local (a)biotic habitat characteristics, and a typical seep meiofaunal community cannot be delineated. Stable isotope values suggested the nematode diet up to 10 m from the seep site included thiotrophic carbon. The thicker hemipelagic sediment layer (photosynthetic carbon), the increased trophic diversity, and the heavier nematode δ13C farther from the seep site suggest a decrease in thiotrophy and an increase in photosynthetic carbon in the nematode diet.