Recently, researchers attracted to studies on the atmospheric pressure plasma jet (APPJ) and their application in medicine and biology. Therefore, the aim of the present study was to evaluate total protein and protein profile exchange in Eisenia fetida and Aporrectodea trapezoides earthworm after exposed to APPJ for different time durations. For this purpose, the levels of total protein and protein profile in E. fetida and A. trapezoides that exposed to 0 (as a control), 5, 10, 20 and 30 second of APPJ were assessed by Bradford and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) methods, respectively. The results showed, the highest level of total protein were at control groups of the E. fetida and A. trapezoides. Also protein pattern were changed in both species after exposure to APPJ. All specimens of groups were survived after exposure times. The experimental results suggest that the APPJ can be change in the protein expression in earthworms, while that E. fetida is more sensitive than A. trapezoides.