Native oceanic biodiversity is under threat worldwide due primarily to anthropogenic factors such as rising ocean temperatures and the introduction of non-native invasive species. One area which continues to be impacted by these threats is the Gulf of Maine, a region which is warming far more rapidly than most oceanic areas. This marine community is also threatened by invasive species such as Botrylloides violaceus, a colonial ascidian that has colonized large parts of the eastern coastline of the United States. To better understand the mechanisms behind this colonization, we investigated habitat associated changes in gene expression which might underlie this species’ ability to adapt to non-native climates. We extracted RNA from colonies of B. violaceus from two locations: Nubble Point, ME, a near shore environment, and Isles of Shoals, NH, an offshore environment, collecting three colonies of B. violaceus from above and below the thermocline at each site. By comparing gene expression profiles across site and depth, we have identified a host of candidate genes which may be integral in this species’ successful adaptation to multiple habitats, including genes involved with stress response such as universal stress protein A-like and META2, genes associated with osmoregulation, including calcium and sodium transport proteins, and thermoregulation genes such as HSP30, HSPA12A, and HSPB6. These results suggest the acclimatization of B. violaceus to non-native climates may be associated with environmentally induced variation in gene expression and provide new directions for future research into the molecular mechanisms underlying the spread of invasive species.