The aim of this study was to determine the occurrence of the most representative cyclic imines (CIs) gymnodimine (GYM), pinnatoxin G (PnTX-G), and 13-desmethyl SPX C (SPX1) in Mediterranean mussels (Mytilus galloprovincialis Lamarck, 1819) (n = 416), European oysters (Ostrea edulis Linnaeus, 1758) (n = 104), Queen scallops (Aequipecten opercularis Linnaeus, 1758) (n = 52) and edible ascidians of the Microcosmus spp. (n = 104) originating from nine harvesting and breeding areas in the northern part of the Adriatic Sea using ultra-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS). All CI concentrations were far below the guidance level of 400 μg SPXs/kg proposed by the EU Reference Laboratory for Marine Toxins. In contrast to Queen scallops and ascidians, in Mediterranean mussels and European oysters CIs were found throughout the year. Our data reveal the differences between species predisposed for CIs accumulation, as well as seasonal and locational variations in CIs occurrence.