We measured the concentrations of antifouling biocides in sediment, mangrove leaves and seagrasses from Merambong and Tinggi Island, Johor, Malaysia to evaluate their contamination levels. Although the concentrations of tributyltin (TBT) in mangrove leaves in Merambong in 2013 were significantly lower than those in 2012, the Sea-Nine 211 concentration in 2013 was significantly higher than that in 2012, suggesting that the use of antifouling biocides changed from TBT to Sea-Nine 211. The concentration of each BT (butyltin) and PT (phenyltin) in the mangrove area was significantly higher than the corresponding concentration in the seagrass area in Merambong, but the concentrations of Sea-Nine 211, diuron, chlorothalonil, Irgarol 1051 and M1 in seagrasses were significantly higher than those in mangrove leaves. There were differences in the accumulation profiles of OTs (organotins) and alternative biocides between the seagrass shoots and roots. The concentration of OTs in the seagrass roots was almost the same or higher than those in the shoots, whereas those of alternative biocides shows the opposite pattern to the OTs. Significant high relationships were observed between stable carbon isotope (δ13C) and OTs, Sea-Nine 211 and Irgarols in mangrove leaves. The concentrations of these compounds increased along with the δ13C values of the mangroves. These results suggest that mangroves take up the bicarbonate ions and nutrients in sediment and/or seawater through their roots, along with OTs, Sea-Nine 211 and Irgarols which were accumulated in sediment.