Mercury (Hg) is a toxic element and has no known biological functions in humans. This study measured total Hg and methyl mercury (MeHg) concentrations in commonly consumed fish and seafood as well as to estimate the risk of Hg contamination through seafood consumption by Malaysians. The concentrations of total Hg and MeHg in 8 species of crustaceans (n = 15), 5 species of cephalopods (n = 12), and 29 species of fish (n = 78) from West Peninsular Malaysia are reported. Total mercury concentrations in crustaceans, cephalopods and fish were 0.033 ± 0.033 μg/g, 0.040 ± 0.025 μg/g and 0.106 ± 0.128 μg/g wet weight respectively. The proportion of methyl mercury in fish was 81–99% with a mean of 93 ± 5% (n = 15). Significantly higher mercury concentrations were observed in demersal fish, fish on higher trophic level and fish with body length of >20 cm. All fish and seafood were below the Malaysian Food Regulations of 0.5 μg/g wet weight mercury for fish and fishery products and 1.0 μg/g wet weight mercury for predatory fish. The consumption of fish from certain seafood species, however, should be taken into consideration to ensure that the Provisional Tolerable Weekly Intake (PTWI) of MeHg does not exceed 1.6 μg/kg body weight/week.