Fish contain important polyunsaturated fatty acids (PUFA) that are mostly obtained from their diets and subsequently transferred to higher consumers, including humans. Mercury is taken up by all aquatic organisms and may threaten the benefits imparted by fish. Both mercury (Hg) and PUFA occur together in dietary sources for fish, and both are conveyed along aquatic food webs.The eutrophic status of aquaculture units (ponds, reservoirs) in China and elsewhere can also impact fish Hg bioaccumulation and PUFA profiles.And the eutrophication may lower the high-quality PUFA content in fish by changing the plankton community composition. To assess the effect of aquaculture on the fatty acids composition and potentially toxic mercury (Hg)content in fish, we investigated total mercury (THg), methylmercury (MeHg),polyunsaturated fatty acids, including eicosapentaenoic (EPA,20:5n−3) and docosahexaenoic acid (DHA, 22:6n−3) in cultured and wild fish and their potential diets from two reservoirs in southwest China. In cultured fish, mercury contents were lower, but EPA+DHA and omega-3 to omega-6 and (n-3/n-6) PUFA ratios were higher than in wild fish. The lower Hg content in cultured fish was related to the lower Hg in fish feeds and Hg bio-dilution due to the higher somatic growth mainly contributed by the higher DHA contents in fish feeds. As assessed by highly valuable PUFA and potentially toxic Hg contents, these results suggest that these cultured fish had higher nutritional value than wild fish. However, the EPA+DHA content and n-3/n-6 PUFA ratios were lower in plankton from aquaculture reservoirs, implying that aquaculture may change the community structure of the pelagic food, lower the PUFA content in plankton, and consequently reduce dietary PUFA transfer to upper trophic levels.