The present work aims to determine and compare the tolerance to different stress environmental conditions in two crabs’ species the native Carcinus aestuarii and the invasive Portunus segnis. In this study, C.aestuarii appeared more intolerant to environmental stressor as shown by the important changes occurred on the proximate, fatty acids and their essential compounds comparing to P.segnis. Our results revealed accumulation of metallic trace elements, macromolecular damages and antioxidant defense systems perturbations mostly in C.aesuarii gills and muscles than P.segnis, thus highlighting the importance of a multi-markers approach to assess the urban pollution in coastal ecosystems. According to this study, fatty acid profiles and oxidative stress biomarker examination of both crabs indicate that the different environmental stresses significantly influence the tolerance of C.aestuarii compared to the invasive P.segnis which may provide physiological advantages for the achievement of their invasion in novel ecosystems.