This study aims to determine the variety of ectoparasites in Puntius sp. and Anabas sp. fish from aquaculture activities. A total of 60 Puntius fish and 60 Anabas fish were taken for examination of ectoparasites on the gills and body surface. A total of 4 ectoparasites were found to infest Puntius fish, namely Trichodina (78.3% in prevalence), Ichthyopthirius multifiliis (10% in prevalence), Dactylogyrus (50% in prevalence), and Gyrodactylus (15% in prevalence); while 5 ectoparasites were found to infest Anabas fish, namely Ichthyopthirius multifiliis (8.3% in prevalence), Trichodina (61% in prevalence), Dactylogyrus (45% in prevalence), Argulus japonicus (5% in prevalence), and Lernaea cyprinacea (1.6% in prevalence). Trichodina is the parasite found in greatest abundance in both endemic fishes.There were differences in the number, type and prevalence of ectoparasites infesting the two endemic farmed fish. Trichodina was found with the highest prevalence in both endemic fish species farmed in Indonesia. This is the first finding to provide an understanding of the types and patterns of ectoparasite infestation in the two species of wader farmed in Indonesia.