In this paper we present the results of research on the occurrence, induction and role of photoprotective compounds (PPCs) present in native aquatic yeasts from freshwater Patagonian ecosystems. We focus on the effect of UV radiation (UVR) as a factor that controls the level of photoprotection of yeasts, and explore its potential significance in shaping yeast distributional patterns. The research presented here combines field surveys and laboratory work, including the isolation and culture of native yeasts strains, and laboratory assays under different radiation conditions. The results obtained suggest that yeasts are common dwellers of oligotrophic Patagonian water bodies, and provide the first evidence of the distribution of PPC (carotenoid and mycosporine)–producing yeasts in temperate freshwaters. A greater proportion of carotenogenic yeasts were observed in high-elevation lakes. The yeast strains isolated from these environments were found to produce higher amounts of mycosporines (MYCs), and to present higher tolerance to UVB exposure than those from piedmont lakes. Patagonian yeasts have only one type of MYC, mycosporine-glutaminol-glucoside (myc-glu-glu), which seems common to all other yeasts. By analyzing the production of myc-glu-glu in a large number of yeasts belonging to different taxonomic groups, we propose that this compound may have potential use as a chemotaxonomic marker in yeast systematics. Collectively, our work reveals that in Patagonian freshwater yeasts there is an apparent relationship between the ability to produce PPCs, their tolerance to UV exposure and their success in colonizing habitats highly exposed to UVR.