We explored the possible mechanisms leading to differential Cd sensitivity in three marine phytoplankton (the diatom Thalassiosira pseudonana, the dinoflagellate Prorocentrum minimum and the green alga Chlorella autotrophica) based on their Cd accumulation, Cd subcellular distribution, and phytochelatin (PC) synthesis. The most sensitive species, T. pseudonana, generally exhibited the highest Cd body burden and organelle (org)-Cd concentration. C. autotrophica, the most tolerant species to Cd, had the smallest org-Cd accumulation, as well as a much higher percentage of cellular debris-Cd, which may play an important role in Cd detoxification. The dinoflagellate P. minimum, with a sensitivity between the diatoms and green algae, had a comparable Cd body burden but higher percentage of org-Cd than C. autotrophica. Although the induction of PCs was dependent on the species, the intracellular (intra)-Cd/PC-SH ratio showed a strong linear log-log relationship with [Cd(2+)], suggesting that this ratio could possibly be a biomarker for environmental [Cd(2+)] stress. With the increases of the intra-Cd/PC-SH ratio, these three species of phytoplankton exhibited clearly different patterns of growth inhibition, implying that the effectiveness of PCs as a detoxification pathway is dependent on the species. The lowest intra-Cd/PC-SH toxicity threshold for T. pseudonana implied its low PC-Cd capacity. Furthermore, the sudden slowdown of growth inhibition when the intra-Cd/PC-SH ratio reached 33 implied the launch of other detoxification pathway in C. autotrophica in order to alleviate Cd toxicity. Our study demonstrated that accumulation and subcellular distribution of Cd and PC synthesis can account for the inter-species differences in Cd sensitivity in marine phytoplankton.