This study assessed total selenium concentrations (TSe) in the muscle tissues, liver and gonads samples of three fish species (Mugil liza - mullet, planktivorous fish; Bagre spp. - catfish, omnivorous fish and Micropogonias furnieri - Atlantic croaker, carnivorous fish) and also in the soft tissues of a mussel (Perna perna) from Guanabara Bay. TSe in the digested samples was analyzed by GF-AAS using Zeeman background correction. Pd was the chemical modifier. The analytical methodology presented high precision and accuracy when tested with certified reference materials, DORM-2 and NIST 2976, and also through intercomparison between two laboratories, Laboratório de Radioisótopos (UFRJ) and a reference laboratory from a Finish National Public Health Institute, using fish samples. The liver samples of all studied fish species presented the highest TSe. Carnivorous and planktivorous fishes presented similar TSe in their liver. Carnivorous fish showed the highest TSe in the muscle. The muscle was the only tissue that presented a direct influence of the feeding habits. Carnivorous and planktivorous fishes showed high positive correlations between TSe in the muscle and their total length, age and consequently, with the exposure time at environment. A significant correlation was observed between the selenium concentration in the mussel soft tissues and the condition index (IC). We verified in the scientific literature that our study was the second one conducted in Brazil. Furthermore it was the first one that compared the total selenium concentrations in organs and tissues of several aquatic organisms with different feeding habits.