Is there a mesopelagic protist fauna composed of species different from that of the overlying surface community? Does the mesopelagic community show seasonal changes in abundances and species composition? We addressed these questions by considering three distinct groups in which species identification is relatively unambiguous: tintinnid ciliates, phaeodarian radiolarians, and amphisolenid dinoflagellates. We sampled weekly at 250 m and 30 m depth from January to June a deep-water coastal site characterized by seasonal changes in water column structure; notably, in winter the mixed layer extends down into mesopelagic depths. We found a deep-water community of tintinnid ciliates comprised of forms apparently restricted to deep waters and species also found in the surface layer. This latter group was dominant during the winter mixis period when tintinnid concentrations were highest and subsequently declined with water column stratification. Phaeodarian radiolarians and the amphisolenid dinoflagellates were regularly found in deep samples but were largely absent from surface water samples and showed distinct patterns in the mesopelagic. Phaeodarian radiolarians declined with water column mixing and then increased in concentration with water column stratification whilst amphisolenid dinoflagellates concentrations showed no pattern but species composition varied. We conclude that for all three protists groups there appear to be both distinct mesopelagic forms and seasonal patterns.