Mud volcanoes are a special type of cold seeps where life is based on chemoautotrophic processes. They are considered as extreme environments and are characterised by unique megafaunal and macrofaunal communities. However, very few studies on mud volcanoes taking into account the smaller meiobenthic communities have been carried out. Two mud volcanoes were explored during the MEDECO cruise (2007) with the Remotely Operated Vehicle (ROV) Victor-6000; Amsterdam, located south of Turkey between 1700 and 2000 m depth (Anaximander mud field) and Napoli, south of Crete, located along the Mediterranean Ridge at about 2000 m depth (Olimpi mud field). The major aim of this study was to describe distributional patterns of meiofaunal communities and nematode assemblages from different seep microhabitats. Meiofaunal taxa and nematode assemblages at both mud volcanoes differed significantly from other Mediterranean sites in terms of standing stocks, dominance and species diversity. Density and biomass values were significantly higher at the seep sites, particularly at Amsterdam. Nematodes, the dominant meiofaunal taxon, displayed deeper penetration vertically into the sediment at the seep areas, indicating that biological rather than physicochemical factors are responsible for their vertical distribution. Patterns of nematode diversity varied, displaying both very high or very low species richness and dominance, depending on the habitat studied. The Lamellibrachia periphery and mussel bed of Napoli exhibited the highest species richness while the reduced sediments of Amsterdam yielded a species-poor nematode community, dominated by two successful species; one belonging to the genus Aponema and the other to the genus Sabatieria. Analysis of β-diversity showed that habitat heterogeneity of mud volcanoes contributed substantially to the total nematode species richness in the eastern Mediterranean Sea. These observations indicate a strong influence of mud volcanoes and cold-seep ecosystems on the meiofaunal communities and nematode assemblages.