Zooplankton species have evolved several adaptive strategies to minimize damage caused by exposure to solar ultraviolet radiation, but the environmental conditions favoring one strategy or another are not yet fully understood. Here, I quantified the concentration of photoprotective compounds (carotenoids and mycosporine-like amino acids or MAAs) and assessed the photorepair activity (photolyase assay) in populations of the calanoid copepod, Arctodiaptomus jurisowitchi and the cladocerans, Daphnia himalaya and D. longispina, from five high altitude lakes located in the Himalayan Region (Khumbu Valley, Nepal) between 4890 and 5440 m above sea level. The concentration and diversity of MAAs were low in copepods, as well as in seston samples. Significant differences in the concentration of MAAs among the five copepod populations were largely explained (96%) by the lake depth refuge (i.e., the fraction of the water column to which 1% of the surface UVR at 320 nm penetrates). Concentrations of carotenoids (mostly free astaxanthin) in copepods were among the highest reported in the literature. Similar to MAAs, the carotenoid concentration was inversely related to the lake depth refuge. The lowest concentration of photoprotective compounds in copepods was observed in a turbid glacier lake, whereas the highest was found in a shallow water body dominated by a benthic mat of filamentous green algae. Except for the presence of melanin in D. himalaya, no other photoprotective compounds were found in cladocerans. The assay of photolyase activity in A. jurisowitchi and D. himalaya suggested the absence of a photorepair mechanism. The results of this study indicate that the copepod populations from this relatively pristine alpine region rely mainly on the accumulation of carotenoids to minimize damage by UV radiation, a pattern that strongly contrasts with what is known for copepods from other alpine lakes, for instance, in the Alps. I hypothesize that this difference is attributed to nitrogen limitation of the MAA synthesis in phytoplankton from remote Himalayan lakes.