Sediment is the ultimate reservoir of effluent from landmasses. This includes octylphenol (OP) and nonylphenol (NP), two chemical compounds which are known with the ability to disrupt the normal functions of hormones in the organism. To our knowledge, no study of these compounds in the marine sediment of Malaysia has been published to date. Hence, this study presents the level of OP and NP in the sediment of the South China Sea and Malacca Strait, Malaysia. The extraction of compounds was done using the liquid-liquid extraction method and followed by clean-up using solid-phase extraction cartridges. The range of OP in Malacca Strait (1.00-27.16 ng/g dw) was greater than in the South China Sea (5.12-14.16 ng/g dw) whereas a similar range of NP was found in the South China Sea (1.32-23.76 ng/g dw) and Malacca Strait (0.79-27.59 ng/g dw). The concentration of both compounds was consistently high near Redang Island (E2A) and Penang (W32 and W43) suggesting continuous input of these chemicals from this nearby land. Risk quotient (RQ) values of OP showed the potential risk to benthic communities in 4/7 and 21/47 sampling points of the respective South China Sea and Malacca Strait. Both water bodies are located far from the wastewater effluent and yet able to retain these chemicals in their sediment. This suggests that the wastewater treatment system as well as dilution effects do not prevent these chemicals to be ended up in the marine environment.