This study investigates persistent organic pollutants (POPs) in commercially important fish and bivalve species from the coast of Santa Catarina, southern Brazil. We quantified 48 polychlorinated biphenyls (PCBs), 7 polybrominated diphenyl ethers (PBDEs), and 17 chlorinated pesticides (OCPs) in 32 pools of 18 fish species (n = 3 individuals per species of similar size) and 9 pools of 3 bivalve species (n = 12 individuals per species, in total 108 individuals). Approximately 1 g of dry tissue was extracted with n-hexane:dichloromethane using an ultrasonic bath and purified with sulfuric acid. Identification and quantification were performed via injection of 1 μL of extract into a gas chromatograph (Agilent Technologies 7890B) coupled to a triple quadrupole mass spectrometer (Agilent Technologies 7010B) in multiple reaction monitoring (MRM) mode.