Porphyra haitanensis (T. J. Chang & B. F. Zheng) is an important economic alga found off the southern coast of China. It has evolved a strong tolerance against stress, which is an important survival characteristic. Cyclophilin has been shown to be involved in the stress response of plants and algae. To investigate the tolerance against stress in Porphyra, we isolated the cyclophilin PhCYP18 gene (Accession number JQ413239) and measured its expression over different generations and stress conditions. In P. haitanensis, cyclophilin PhCYP18 accumulated more in the filamentous sporophyte generation than in the blade gametophyte generation. This difference was thought to be due to harsh environments and a gene dosage effect. It has been found, however, that PhCYP18 expression was dysregulated in blades under high salt stress, strong irradiance stress and multifactorial stress compared to blades under normal conditions. Moreover, the changes were not linearly related to the degree of stress. It was therefore thought that PhCYP18 actively responded to stress situations and induced strong stress tolerance, which is evident in P. haitanensis.