Irgarol 1051 is highly toxic to marine autotrophs and has been widely used as an antifouling booster biocide. This study tested the toxicities of two s-triazine derivatives of Irgarol, namely M2 (3-[4-tert-butylamino-6-methylthiol-s-triazin-2-ylamino]propionaldehyde) and M3 (2-methylthio-4,6-bis-tert-butylamino-s-triazine) to two marine diatom species, Skeletonema costatum and Thalassiosira pseudonana through standard acute (96h) and chronic (7d) growth inhibition tests. Results showed that both of the two chemicals significantly inhibited the growth of S. costatum (M2: 96h-EC50 = 6789.7 μg L−1, 7d-EC50 = 3503.7 μg L−1; M3: 96h-EC50 = 45193.9 μg L−1, 7d-EC50 = 5330.0 μg L−1) and T. pseudonana (M2: 96h-EC50 = 366.2 μg L−1, 7d-EC50 = 312.5 μg L−1; M3: 96h-EC50 = 2633.4 μg L−1, 7d-EC50 = 710.5 μg L−1), while their toxicity effects were much milder than Irgarol and its major degradation product M1. By comparing with previous findings, the susceptibilities of these s-triazine compounds to two tested species were ranked as: Irgarol > M1 ≫ M2 > M3. This study promotes future research efforts on better understanding of the ecotoxicities of M2 and M3, and incorporating such information to improve the current monitoring, risk assessment and regulation of the use of Irgarol.