Protein modification process through ubiquitination system is a potential goal for developing genetic improvement strategies of plants under different stress conditions. To identify the ubiquitinated proteins and related pathway involved the thermotolerance of an importantly economic and ecological seaweed, Pyropia haitanensis, the present study performed quantitative ubiquitylome crosstalk with proteome analysis of a thermotolerance strain (WO72-4) exposed to high temperature stress.