Abstract: Forty-eight surface sediment samples were collected from typical sea areas of Beibu Gulf Rim between April 2015 and May 2016. Biogenic elements including total organic carbon (TOC), total nitrogen (TN), total phosphate (TP) and biogenic silica (BSi) were analyzed. The concentrations of TOC, TN, TP and BSi were in the range of 0.27%~1.64%, 0.09%~0.25%, 0.02%~0.05% and 0.55%~2.28%, respectively. Biogenic elements were higher in Zhanjiang port, and followed by Beihai port. Concentrations of TOC, TN, and TP were comparable in four ports of Hainan coast, however BSi levels were significantly higher in Haikou port and Xinhai port in the northern coast than those in Yangpu port and Basuo port in the mid-western coast. The significant coefficients among biogenic elements indicated their similar origin. TOC mainly originated from marine phytoplankton especially from diatoms based on the molar ratios of TOC/TN. Contamination assessment of biogenic elements indicated TN was contaminated in all ports, and TOC in Zhanjing port, Beihai port and Baosuo port has been polluted as well.