Bathyal cold seeps are isolated extreme deep-sea environments characterized by low species diversity while biomass can be high. The H?kon Mosby mud volcano (Barents Sea, 1280 m) is a rather stable chemosynthetic driven habitat characterized by prominent surface bacterial mats with high sulphide concentrations and low oxygen levels. Here, the nematode Halomonhystera hermesi thrives in high abundances (11,000 ind. 10 cm(-2)). Halomonhystera hermesi is a member of the intertidal H. disjuncta species complex that includes five cryptic species (GD1-5). GD1-5's common habitat is characterized by strong environmental fluctuations. Here, we compared the transcriptomes of H. hermesi and GD1, H. hermesi's closest relative. Genes encoding proteins involved in oxidative phosphorylation are more strongly expressed in H. hermesi than in GD1, and many genes were only observed in H. hermesi while being completely absent in GD1. Both observations could in part be attributed to high sulphide concentrations and low oxygen levels. Additionally, fatty acid elongation was also prominent in H. hermesi confirming the importance of highly unsaturated fatty acids in this species. Significant higher amounts of transcription factors and genes involved in signalling receptor activity were observed in GD1 (many of which were completely absent in H. hermesi), allowing fast signalling and transcriptional reprogramming which can mediate survival in dynamic intertidal environments. GC content was ca. 8% higher in H. hermesi coding unigenes resulting in differential codon usage between both species and a higher proportion of amino acids with GC rich codons in H. hermesi. In general our results showed that most pathways were active in both environments and that only three genes are under natural selection. This indicates that also plasticity should be taken in consideration in the evolutionary history of Halomonhystera species. Such plasticity, as well as possible pre-adaptation to low oxygen and high sulphide levels might have played an important role in the establishment of a cold-seep Halomonhystera population.