Asian seabass (Lates calcarifer) culture in marine cages have been developed rapidly in Malaysia. The high intensity of culture might facilitate several disease infection including caligid infestation. This study was conducted to evaluate the effect of neem oil (Azadirachta indica) against caligid parasites on seabass. The prevalence and clinical pathogen of Caligus infection has been described through a sampling of 150 fish from floating cage at different cultured periods. Acute toxic tests with different concentrations of neem oil were carried out on the parasite and fish host. Results revealed that the 96‐hr median lethal concentration (LC50) of Caligus and fish (10.3 ± 2.5 g of body weight) were 2 and 20 ppm respectively. The in vivo test indicated that 10 ppm of neem oil could result in 100% antiparasitic efficacy within 96 hr. These results therapeutically demonstrated the efficacy of neem oil in caligid control.