The harsh environments and high biodiversity of the Qinghai-Tibet Plateau (QTP) provide an ideal natural laboratory for studies on adaptive evolution.Low temperature and intense UV-B radiation are the main abiotic stresses to plants at high altitudes.The rapid development of RNA sequencing has enabled us to investigate the molecular adaptations of plants that thrive in the QTP at the genomic level.Despite the ecological importance of Oocystis algae on the plateau,the genetic mechanisms of the adaptations of these algae to this high-altitude environment remain poorly understood.Here,we sequenced and assembled the transcriptomes of Oocystis marina and Oocystis sp.LXD-20,and undertook comparative transcriptomic and evolutionary analyses to reveal their adaptive strategies.Our results identified 348 positively selected genes in Oocystis algae,and functional analyses indicated that many of these positively selected genes were associated with adaptation to abiotic stresses,such as antioxidative response,DNA repair mechanisms,translation,and post-translational modifications.We also identified the cold-responsive and UV-B-responsive genes in O.marina and Oocystis sp.LXD-20,and revealed the transcriptional regulation strategies under stress conditions.Our analyses provided a wealth of sequence data to serve as reference transcriptomes for future studies,and shed light on the adaptive strategies of green algae that live in the QTP.