The ascidian species Ciona savignyi and C. intestinalis are invasive species but show interspecific differences in their population response to hypo-saline stress associated with heavy winter-run off events that are predicted to become more frequent due to climate change. Despite an almost world-wide distribution, C. intestinalis seems to be more susceptible to hypo-saline stress than the geographically more limited C. savignyi. Given that the genomes of both species are fully sequenced, we were able to compare their proteomic response to both acute and chronic salinity to characterize the mechanisms that are responsible for setting tolerance limits to hyposaline conditions in these two congeneric species. For the acute hypo-saline stress experiment, we exposed each species to decreasing salinities, 100%, 85% and 70% full-strength seawater, for 6 hours followed by a 4-hour recovery at 100%. In the chronic salinity stress experiment, each species was kept at 100% or 85% with individuals removed for analysis during a 16-day time course. Organisms were dissected to remove the tunic, and 2D SDS-PAGE was performed to separate proteins and characterize changes in protein abundances. In the acute experiment, we determined 5% and 19% of the proteins to be significantly changing abundance in C. savignyi and C. intestinalis, respectively, due to the treatment effect. For both species in the chronic experiment, we determined over 40% of the proteins to be significantly changing abundance given the treatment, time, or interaction effect. Analysis of these proteins with MALDI TOF-TOF mass spectrometry has identified numerous proteins implicated in cellular stress responses, including energy metabolism (glycolysis, ATP & NADH production), cytoskeletal restructuring, and protein turnover, providing insights into the intense cellular restructuring that occurs following hypo-saline exposure.