This study compares the chemical composition of cockle (Anadara granosa) and some commercially important marine (Asian seabass Lates calcarifer, grouper Epinephelus bleekeri, hardtail scad Megalaspis cordyla, longtail tuna Thunnus tonggol and Indian mackerel Rastrelliger kanagurta) and freshwater (sutchi catfish Pangasius hypophthalmus, Nile tilapia Oreochromis niloticus and eel Monopterus albus) fishes in Peninsular Malaysia. The results show that the proximate composition and trace metal content were significantly different (P < 0.05) among species investigated. The mean protein content was the highest in eel (19.1%) and the lowest in sutchi catfish (13.0%) and cockle (13.0%). The mean lipid content of Indian mackerel (3.9%) was higher than cockle (2.0%), followed by eel (1.3%) and longtail tuna (0.8%). The mean ash content was the highest in Indian mackerel (1.4%) and the lowest in cockle (0.9%). Zinc and manganese contents in cockle (Zn: 61.2 mg kg−1, Mn: 22.7 mg kg−1) were very high compared to other species investigated. The copper content was minimum in sutchi catfish (1.0 mg kg−1) and a maximum in the hardtail scad (11.7 mg kg−1). Trace metal content in sutchi catfish, Nile tilapia, grouper, longtail tuna, eel and cockle followed an order Zn > Mn > Cu, whereas Asian seabass, hardtail scad and Indian mackerel followed a different order Zn > Cu > Mn. Trace metal content in the tissue of the fishes examined was within safe limits for human consumption except Mn content in the cockle and Cu content in the hardtail scad, which is a matter of concern. When considering the daily fish fat, mineral and trace metal intake, marine fishes and shellfish are better than freshwater fishes.