Four hundred Chrysichthys nigrodigitatus were examined for protozoan parasites using saturated saline bath, mild formalin bath, saturated saline floatation and method described for histopathology. Seventy (17.5%) infection was recorded. Forty two (10.5%) and Twenty eight (7.0%) were constituted by Chilodonella sp and Trichodina sp respectively. The two parasites occurred on the skin and gills respectively. Chilodonella was evident on the skin by dilated mucus pore and excessive mucus secretion by the infected fish. In addition to excess mucus on gill of fish infected by Trichodina sp, hypertrophy of the gill filament was observed. While highest prevalence of Chilodonella sp (10.8%) was observed during wet season. Trichodina occurred mostly (18.2%) during dry season. Chilodonella sex parasitism favoured female fish while that of Trichodina favoured male fish. Parasite intensity and condition factor decreased with length. Marketed fish should be examined to ensure parasite free fish protein presented for public consumption.