Two nematode species living in association with chemoautotrophic prokaryotes were found in two deep-sea canyon/channel systems, the Whittard Canyon and Gollum Channels, north-east Atlantic. Parabostrichus bathyalis gen. nov. sp. nov. (Desmodorida: Desmodoridae: Stilbonematinae) relates to Eubostrichus Greeff 1869 but differs in having well-developed paired dorso-caudal apophyses of the gubernaculum, small pre- and postcloacal latero-ventral papillae with short apical setae, elongate tail with slender posterior portion, and the absence of thorn-like setae (porids) in males. Body of P. bathyalis is loosely covered with elongate cells of prokaryote ectosymbionts. Astomonema southwardorum Austen et al. 1993, originally found at a methane seep pockmark in the North Sea, constitutes a significant portion of nematode communities in certain areas of the deep-sea canyon/channel systems. Taxonomic difficulties within Astomonematinae are discussed in light of the character state of paired male gonads discovered in A. southwardorum. Canyon populations of A. southwardorum are characterized by frequent loss of part of the hind body and wound healing posterior to the vulva in females. Both species tend to occur in deeper subsurface layers of the bottom sediment. Abundance of the nematode species associated with aggregations of ectosymbiotic (Parabostrichus) and endosymbiotic (Astomonema) chemoautotrophic bacteria may indicate reduced conditions at sites in these deep-sea canyons/channels and suggests a potentially substantial ecological role for chemolitotrophic fauna there.