This study provides a dataset of rare earth elements (REEs) in the seawater of Sulu and Celebes Seas of Malaysian waters during the PMSE 09' expedition, which was conducted to define the pattern of REEs in both seas on-board ship then analyzed by using ICP a high concentration of REEs in vicinities with high number of local Island riverine flush-outs. The chemometric analysis has sites between REEs and salt ions. influence of South China Sea waters l studied area shows that both seas are affected by local river Indonesia and Philippine archipelagos.