A family of antimicrobial peptides (AMPs) derived from the beta-subunit of haemoglobin was recently isolated from channel catfish, Ictalurus punctatus, infected with Ichthyophthirius multifiliis (ich), an important freshwater fish parasite that causes ichthyophthiriosis. We previously discovered that one of these AMPs, HbbetaP-1, had strong cidal activity against ich as well as another ectoparasite, Tetrahymena pyriformis. HbbetaP-1 toxicity was specific, primarily affecting the trophozoite (trophont) stage of ich. Here, we show that HbbetaP-1 acts more rapidly to kill smaller (presumably less mature) trophonts of ich, taking almost twice as long to kill larger trophonts (P < 0.0001). It acts more rapidly than an unrelated AMP, piscidin 1, which is haemolytic and also lethal to ich trophonts. HbbetaP-1 is potently and selectively lethal to the trophont stage of the dinoflagellate ectoparasite, Amyloodinium ocellatum, one of the most important pathogens of warmwater marine fish. HbbetaP-1 has no effect on the fish gill cell line feeder layer (G1B cells) used to propagate Amyloodinium, further suggesting a highly selective action. These findings suggest that HbbetaP-1 or related AMPs might function in protecting marine as well as freshwater fish and that HbbetaP-1 has highly selective activity against specific life stages of important fish ectoparasites.