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Differently fed groupers Epinephelus coioides from an Indonesian finfish mariculture farm were studied for ecto- and endohelminth parasites. Pellet-fed E. coioides were infested with 13 parasite species/taxa of which six had a monoxenous and seven a heteroxenous life cycle. A total of 14 parasite species/taxa were found in the fish that were fed with different trash fish species, four of them with a monoxenous and ten with a heteroxenous life cycle. The use of pellet food significantly reduced the transfer of endohelminths and the number of parasites with a heteroxenous life cycle. Out of ten studied trash fish species, 62 parasite species were isolated (39% ectoparasitic and 61% endoparasitic), four of them also occurring in the cultured E. coioides and 14 in different groupers from Balai Budidaya Laut Lampung. The trash fish is held responsible for the transmission of these parasites into the mariculture fish. Endohelminth infestation of pellet fed fish demonstrates that parasite transfer also occurs via organisms that naturally live in, on, and in the surroundings of the net cages. Seventeen recorded invertebrates from the net cages might play an important role as intermediate hosts and hence parasite transmitters. The risk of parasite transfer can be considerably reduced by feeding selected trash fish species with a lower parasite burden, using only trash fish musculature or minimizing the abundance of invertebrates (fouling) on the net cages. These methods can control the endoparasite burden of cultivated fish without medication. The control of ectoparasites requires more elaborate techniques. Once they have succeeded in entering a mariculture farm, it is almost impossible to eliminate them from the system.