The proteomic changes occurring during speciation are fundamental to understand this process, though they have been rarely addressed until present. Therefore, we compared the proteome of two ecotypes (RB and SU) of the marine snail Littorina saxatilis, a case of sympatric incomplete speciation, originated as a byproduct of adaptation to distinct habitats. Thus, the RB ecotype is able to resist stresses of desiccation and temperature on the upper shore, whereas the SU ecotype defies strong physical disturbances due to wave action. Qualitative analyses of 2-DE gels demonstrated 21 proteins differentially expressed (1.4% of the proteome, 1.2% after considering type-I errors), while quantitative changes accounted for differences in 22 spots (16% of the proteome, 11% after considering type-I errors). These results suggest that adaptative phenotypic plasticity, natural selection, or both maintain these ecotypes in sympatry. Among the proteins identified by MS, we found that fructose-bisphosphate aldolase and arginine kinase were up-regulated in the SU ecotype, suggesting an enhancement of the level of energy available as ATP, in order to withstand its wave-exposed habitat.