The present study was undertaken to investigate the diversity and prevalence of the parasites of Synodontis clarias (LINNAEUS, 1758) from Lekki Lagoon, Lagos, Nigeria. S. clarias (the upside-down red-tailed catfish) is a bottom feeder in its natural habitat feeding as an omnivore. It is one of the rich aquatic fauna of the Lekki Lagoon. A total of one hundred and twenty (120) randomly selected fishes were examined for ectoparasites, gastrointestinal parasites, and haemoparasites. A total of nine hundred and sixty-nine (969) gastrointestinal parasites were recovered from the fishes examined. They are two Caryophyllidae cestodes and a Proteocephalid cestode, belonging to the genus: Wenyonia, Caryophyllaeus, and Proteocephalus. Balantidium sp < /em> was found in the intestine of two of the fishes examined. The haemoparasite isolated from the infected fishes was Trypanosoma sp < /em>. The monogenean Gyrodactylus sp < /em> was also recovered from the skin and gills of some of the fishes examined. The overall prevalence of infection was 54.1% for gastrointestinal helminths and 19.1% for haemoparasites. Prevalence of infection was higher in the males than in the females of S. clarias. Histologic examination of infected intestinal tissues showed alterations such as an increase in the connective tissue of the submucosa, stunting of the villi, and loss of intestinal glands.