The responses to waterlogging stress of two wheat genotypes including one sensitive and one resistant were systematic investigated. The labeling-based quantitative proteomic analysis was conducted in parallel on these two genotypes in responding to waterlogging for 1-3 days, 951 and 320 differentially expressed proteins (DEP) were detected in the during treat, and 270 DEPs were shared. The results might help to reveal the regulatory mechanism of waterlogging stress tolerance in wheat.