The sensitivity to ultraviolet radiation (UVR, 280–400 nm) of ten species of freshwater and marine phagotrophic protists was assessed in short-term (4 h) laboratory experiments. Changes in the motility and morphology of the cells, as well as direct quantification of DNA damage, were evaluated. The net amount of cyclobutane pyrimidine dimers formed after exposure of the organisms to a weighted dose (Setlow DNA normalized at 300 nm) of 1.7 kJ m⁻² was quantified by an immunoassay using a monoclonal specific antibody directed against thymine dimers (T<>Ts). This is the first application of this method to aquatic protists. The results indicated that marine and freshwater heterotrophic nanoflagellates, representatives from the order Kinetoplastida (Bodo caudatus and Bodo saltans, respectively) accumulate significantly higher DNA damage than protists representatives of the orders Chrysomonadida, Cryptomonadida or Scuticociliatida. The high proportion of A:T bases in the unique kinetoplast DNA, may explain the higher accumulation of T<>Ts found in bodonids. Experiments made with B. saltans to study the dynamics of DNA damage accumulation in the presence of UVR and photorepairing light, indicated that the mechanisms of DNA repair in this species are very inefficient. Furthermore, the dramatic changes observed in the cell morphology of B. saltans probably compromise its recovery. Our results show that sensitivity to UVR among aquatic phagotrophic protists is species-specific and that different cell targets are affected differently among species. While DNA damage in B. saltans was accompanied by motility reduction, altered morphology, and finally mortality, this was not observed in other bodonids as well as in the other species tested.