Twenty wild groupers ( Cephalopolis boenak) and 20 cultured groupers (Epinephalus tauvina) were used as the main research material in this study. All of these groupers were examined for individual body weight, total length and ectoparasite number and prevalence before and after transportation. The results of this study showed that the four groups of ectoparasite that infected both groups offish were six species namely Ciliated Protozoa; Cryptocaryon i"itans, Trichodina sp., and Unidentified Ciliates, Monogenea; Pseudorhabdosynochus sp., Leech; Zeylanicobdella arogamensis and Parasitic Copepod; Caligus sp. The dominant species for culture grouper is unidentified ciliates meanwhile for the wild grouper is Trichodina sp. Cultured groupers showed an increase in ectoparasites after transportation. Overall comparison showed that cultured groupers maintained the prevalence of ectoparasite before and after transportation with 100% infection; mean intensity showed an increase from 7 .1 before to 37.4 after transportation compared to Wild Grouper with the prevalence of ectoparasite; 65% infection before and 95% infection after transportation and mean intensity of; 3 .2 before and 5 .1 after transportation. The increase in ectoparasite infection could be attributed to change in water quality.