This study was carried out on 120 Synodontis filamentosus sample (11 – 26.5cm, 22 - 88g) and 120 Tilapia zillii fish  (15 - 21cm, 67 – 187g) captured from Epe Lagoon, Lagos State, Nigeria. The aim was to comparatively analyze the bioaccumulation of polybiphenyl chlorides (PCBs) and prevalence of parasitic helminthes in S. sfilamentosus and T. zillii relative to their respective habits. The comparison was done using indices such as bioaccumulation factors, biota-soil accumulation factors, and parasite prevalence. Profiles of PCB accumulation showed that T. zillii followed by their endoparasites accumulated outstanding concentrations, suggesting that T. zillii might be a greater bioaccumulator of PCBs than S. filamentosus. Significant biota-soil accumulation factors observed in the T. zilliii and their endoparasites were accompanied by significant sorption capacities of PCBs into the soil at . This implies that T. zillii accumulated significant PCB from the soil and shared with its endoparasites, justifying host-parasite xenobiotic transfer. S. filamentosus had higher levels of parasitic infections than T. zillii, males of both specieswere more infected than the females. The intestine and liver tissues of S. filamentosus showed greater alterations than the tissues of T. zillii Findings show that S. filamentosus is a better bioindicator in histopathological studies while T. zillii is a better bioaccumulator.