The molecular acclimation of intertidal green macroalga Ulva fasciata Delile to high salinity stress were examined by the construction of a forward cDNA library via the suppressive subtractive hybridization between 30‰ and 90‰ (24 h) and by the time course dynamics of several abundantly expressed genes. Among the genes with known sequences, the expressed sequence tags are abundant in the function of protein synthesis (ribosomal protein) and destination. The cDNAs of ATP-dependent Clp protease (UfClpC), 20S proteasome β-subunit type 1 domain (UfPbf1), ubiquitin-conjugating enzyme E2 I (UfUbc9), and heat shock protein 90A (UfHsp90A) were cloned. UfClpC transcript increased 3 h after 90‰ treatment, followed by a decrease, while UfPbf1 and UfUbc9 transcripts increased after 12 h and decreased at 48 h. The transcripts of UfHsp90A increased 1 h after 90‰ treatment, followed by a drop and to the control level at 48 h. Protease activity increased 3 h after 90‰ treatment and decreased to the control level at 48 h. H₂O₂ contents increased 1 h after 90‰ treatment and then remained unchanged, but protein carbonyl group contents increased after 48 h. The treatments of reactive oxygen species scavengers partially alleviated 90‰ damage (partial growth rescue) and suppressed the increases in H₂O₂ content, protein carbonyl group content, protease activity, and UfClpC, UfPbf1, UfUbc9, and UfHsp90A transcripts by 90‰. The induction of specific chaperones and proteases at the molecular level for protein quality control can be considered as one of the molecular mechanisms of hypersalinity acclimation in U. fasciata.