Commercially important trout species, especially rainbow trout, are under great threat due to several negative factors affecting oxygen levels in water such as global warming and eutrophication. In our study, rainbow trout (Oncorhynchus mykiss) was exposed to chronic (for 28 days) hypoxia (4.0 ± 0.5 mg/L) and hyperoxia (12 ± 1.2 mg/L) in order to evaluate the alteration of fatty acid profiles in muscle, liver and gill tissues. In addition, delta-6-desaturase and elongase gene expression profiles were measured in liver, kidney and gill tissues. The amount of saturated fatty acids increased by oxygen applications in the liver, while it decreased in the muscle and gill tissues compared to normoxia (p < 0.05). Monounsaturated fatty acids levels increased in muscle and gill (p < 0.05). Although n-3 polyunsaturated fatty acid (PUFA) decreased in muscle tissue, n-6 PUFA increased (p < 0.05). The n-3/n-6 ratio decreased in muscle tissue in response to the both exposures (p < 0.05) as well as eicosapentaenoic acid/docosahexaenoic acid ratio (p < 0.05). Hypoxia exposure generally increased delta-6-desaturase and elongase mRNA levels in all tissues (p < 0.05). However, gene expression profiles were variable in fish exposed to hyperoxia. As a result of oxygen exposures, the lipid profile of muscle tissue, which stores dense fat, was negatively affected more than that of liver and gill tissues. We determined that the change in expression levels was tissue specific. Graphical abstract: [Figure not available: see fulltext.].