Dinoflagellates of the genus Amphidinium can produce a variety of polyketides, such as amphidinols (AMs), amphidinoketides, and amphidinin, that have hemolytic, cytotoxic, and fish mortality properties. AMs pose a significant threat to ecological function due to their membrane-disrupting and permeabilizing properties, as well as their hydrophobicity. Our research aims to investigate the disparate distribution of AMs between intracellular and extracellular environments, as well as the threat that AMs pose to aquatic organisms. As a result, AMs containing sulphate groups such as AM19 with lower bioactivity comprised the majority of A. carterae strain GY-H35, while AMs without sulphate groups such as AM18 with higher bioactivity displayed a higher proportion and hemolytic activity in the extracellular environment, suggesting that AMs may serve as allelochemicals. When the concentration of extracellular crude extracts of AMs reached 0.81 µg/mL in the solution, significant differences in zebrafish embryonic mortality and malformation were observed. Over 96 hpf, 0.25 μL/mL of AMs could cause significant pericardial edema, heart rate decrease, pectoral fin deformation, and spinal deformation in zebrafish larvae. Our findings emphasized the necessity of conducting systematic research on the differences between the intracellular and extracellular distribution of toxins to gain a more accurate understanding of their effects on humans and the environment.