The present study illustrates an analysis of histological changes; cadmium (Cd), copper (Cu) and zinc (Zn) accumulation; and metallothionein (MT) levels in normal and deformed Mediterranean killifish, Aphanius fasciatus (Pisces, Cyprinodontidae), collected from unpolluted (S1) and polluted areas (S2) in the Gulf of Gabes in Tunisia. Metal determination in water and sediment showed that the concentrations were significantly higher (p < 0.0001) in S2 compared to S1. Deformed fish showed a significantly higher accumulation of Cd, Cu, and Zn and high levels of MTs in their tissues compared to normal ones. Histopathological investigations revealed greater changes in gills, kidney, liver, and bone tissues of fish from the polluted area than those recorded in fish from the reference area. In comparison to normal fish of the polluted area (S2), tissue alterations were more developed in deformed specimens of this site. A possible relationship between metallic pollution, incidence of spinal deformities, and histological changes in A. fasciatus in the polluted site was discussed.