Metazoan meiofauna and in particular nematode densities, diversity, community structure were studied in relation to water depth (20 m, 50 m, 500 m, 1000 m and 2000 m) along four bathymetric transects in the Western Indian Ocean off the Kenyan coast. Nematode densities ranged between 276–944 ind./10 cm2, which is comparable to values from other oligotrophic areas in the world. Densities was correlated with oxygen concentrations in the overlying water, since they were lowest at mid-depth (500–1000 m) coinciding with the minimum oxygen level. Nematode community structure (at genus level) resembles communities found in temperate slope regions, which are also characterized by a low productivity. The community structure showed correlations with sediment composition, water depth and oxygen levels in the overlying water. Sediment composition was mainly important at the shelf where nematodes separated into a silty sediment-dwelling community with high abundances of Daptonema, Dorylaimopsis,Terschellingia and Halalaimus, and a sandy sediment-dwelling community characterised by high abundances of Microlaimus and Halalaimus. The genera Monhystera, Acantholaimus, Sabatieria, Molgolaimus and Halalaimus dominated the slope communities. The characteristic deep-sea taxa, the monhysterids and Acantholaimus increased in relative abundance with increasing depth, to become dominant at the lower slope (2000 m). The upper (500 m) and mid-slope (1000 m), which coincided with the lowest oxygen concentrations, were colonised by Sabatieria, a genus that is known to inhabit suboxic sediments. Diversity at the level of the genera showed an unimodal trend along the sampled gradient, with highest values at mid-depth (500 m). Although the oxygen minimum at mid depths is much less pronounced than in adjacent areas, the results of this study suggest an impact on the present communities.