The objective of this study is to report the parasitic infections in the gobiid fish with histopathogical changes and the SEM description of the recovered parasites for possible unreported morphological details and for the purpose of control measures in the fish species. Fishes were procured, dissected and examined parasitologically. The nematode, Raphidascaroides sp was the only recovered parasite from the intestine of the gobiid fish. Fixation of the parasites was done in 2.5% glutaldehyde and were post fixed in 1% Osmium tetraoxide, sputter coated and examined with the Scanning Electron Microscope. The infected tissues were also fixed in Bouins fluid.The overall prevalence of infections was 70.7%. Male specimens of the fish species were more susceptible to infections (71.4%) than the female specimens (66.6.) The Raphidascaroides sp. ultrastructure revealed three lips with dentigerous ridges.The two ventrolateral lips measures 68.6 and 69.7 µm while the third lip has a length of 55.1 µm with corresponding breadth of 66.0 µm, 40.5 µm and 59.3 µm respectively. The histopathological alterations in the fish species revealed goblet cell hyperplasia and moderate lymphocytic infiltration of the lamina propria.The dominant and only parasite recovered from the fish host is Raphidascaroides sp, an anisakid nematode whose pathological consequences is mild owing to lack of holdfast organs in nematodes. The ultrastructural description of the parasites is the first report in Nigeria. There is a conclusion that there may be similar food and feeding habits of the fish, Rhinogobius ocellatus with Gymnarchus niloticus with a report of the same parasites in its intestinal mucosa.