Amphidinols (AM) are a diverse group of bioactive polyketides produced by dinoflagellates of the genus Amphidinium, known for their hemolytic, antifungal, and cytotoxic activities. This work presents the assessment of AM profiles in a comprehensive number of strains, whose species boundaries were previously established through detailed taxonomic analysis. Using UHPLC-MS/MS, we characterized the spectrum of AM analogs in 54 Amphidinium strains isolated from diverse geographical locations. In addition, toxicity was assessed using brine shrimp assays, which revealed significant inter- and intraspecific variability. Despite the broad diversity in AM content, no clear correlation was observed between total AM levels and toxicity across all strains. Multivariate analysis grouped the strains into clusters distinguished by distinct AM profiles and toxicity levels, suggesting that AM production alone does not predict toxicity. Our findings highlight the complexity of Amphidinium bioactivity, emphasizing the influence of strain-specific factors and other bioactive compounds. This work highlights the importance of integrating chemical, genetic, and biological assessments to understand better the factors that govern toxicity in this genus, with implications for ecological studies and the monitoring of harmful dinoflagellates.