The genus Amphidinium comprises benthic dinoflagellates with wide geographic distributions and variable ecological and toxicological significance; however, its diversity in Turkish coastal waters remains poorly documented. This study presents a comprehensive morphological, molecular, and toxinological investigation of Amphidinium strains isolated from the Black Sea, the Sea of Marmara, and the Aegean Sea, providing new insights into benthic dinoflagellate diversity in the region. The study was based on a total of 18 cultured strains representing Amphidinium carterae, A. pseudomassartii, A. massartii and A. thermaeum. Among these, A. massartii, A. pseudomassartii and A. thermaeum are reported for the first time from Turkish coastal waters. The occurrence of A. carterae was confirmed across the Black Sea and Sea of Marmara, constituting the first verified records of this species from the Aegean Sea within Turkish coastal waters. Notably, it was the only species detected in all three seas, and its presence across marine systems characterised by contrasting environmental conditions suggests a broad tolerance range and is consistent with a potentially cosmopolitan distribution. Phylogenetic analyses demonstrated complete concordance between all examined strains and globally distributed reference sequences, providing the first molecular validation of these taxa from Türkiye. Targeted toxin analyses revealed a pronounced strain-specific pattern of amphidinol production. Amphidinols were detected in only a subset of A. carterae strains, whereas no amphidinols were identified in the remaining strains or in the other examined species. In conclusion, this study provides the first integrated morphological, phylogenetic, and toxinological assessment of Amphidinium species from Turkish coastal waters and establishes an important baseline for future ecological, phylogenetic, and risk-oriented investigations of benthic dinoflagellates in the region.