The consequences of global change and particularly the interactions between human impacts and warming will presumably alter the structure and functioning of marine ecosystems. In this context, we investigated the stress tolerance of populations of the green mussel (Perna viridis) stemming from two coastal locations in West Java, with different levels of human impact: Jakarta Bay is highly contaminated by nutrient input and pollution, while Tanjung Lesung represents a benign environment with less human influence. In laboratory stress experiments, we determined the mean stress tolerance of the two populations towards reduced salinity by 13 and 18 units, by measuring fluctuations in oxygen consumption, feces production and survival rates. Our results reveal that under reduced salinity responses were significantly different between both populations. In the face of salinity stress mussels from Jakarta Bay showed significantly higher survival and metabolic rates than mussels from Tanjung Lesung, suggesting that the origin of a population contributes substantially to its tolerance towards increasing environmental stress. We discuss possible mechanisms that could underlie these differences in stress tolerance of two populations stemming from different coastal habitats