Outbreaks of heavy infestation by the parasitic dinoflagellate Amyloodinium ocellatum in hatchery-reared milkfish (Chanos chanos) and mangrove red snapper (Lutjanus argentimaculatus) caused 100% mortality events in hatcheries in the Philippines. Parasites were recorded on the body surface in 14-day-old milkfish fry and on both skin and gills in 2-month-old snapper. Trophonts of A. ocellatum caused local erosions of fish skin and degeneration of epithelial cells at the sites of the parasite's attachment to the body surface. Separation and hyperplasia of gill epithelium and fusion of secondary lamellae at the distal parts of the gill filaments were common. High pathogenicity of A. ocellatum to fish may be attributed to the severe alterations of the fish gills, the disruption of the host's skin, and feeding of trophonts on hosts' epithelial cells. In-vivo treatments of A. ocellatum-infested snapper with a 1 h freshwater bath and 200 ppm H₂O₂ showed promising results. This is the first report of A. ocellatum infestation in milkfish and mangrove red snapper in the Philippines.