This study was performed to determine the concentrations of copper (Cu), zinc (Zn), and lead (Pb) in the gill, liver, muscle, and tail fin tissues of Euthynnus affinis, Katsuwonus pelamis, and Thunnus albacares from Oman Sea. All samples were analyzed using a flame atomic absorption spectrophotometer and the results were expressed as μg g −1 dry weight. Metal concentrations were significantly higher in the liver than other tissues in three species (with some exceptions) (p < 0.05). The concentrations of metal accumulation in tissues of tuna species followed the Zn > Cu > Pb. Correlation matrix and principal component analysis (PCA) revealed that Zn and Pb have anthropogenic sources. Estimated daily intake (EDI) in three tuna species for heavy metals were below the tolerable daily intake (TDI). Also, the mean target hazard quotient (THQ) based on studied metals in three tuna species was below 1, which suggests that consumption of these fish can be safe for human health in the Oman Sea.