The accelerated industrialization and urbanization in the last three decades around the Pearl River Delta within Guangdong Province in China have led to serious concerns about the impacts on the aquatic environment. In the present study, the genotoxicity of the sediments collected from the Pearl River was evaluated by micronucleus (MN) assay with Vicia faba root tip cells, and the 16 EPA priority polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs, including Cr, Cu, As, Se, Cd, Hg, and Pb) in the sediments were determined respectively by GC-MS, inductively coupled plasma mass spectrometry, and inductively coupled plasma atomic emission spectrometry. The results showed that there were significant increases of MN frequencies observed in the sediment-exposed groups, compared with the negative group (P < 0.05, P < 0.01), indicating that the sediments clearly had genotoxicity to the V. faba root cells. The total concentrations of the priority PAHs (250-13,656 ng g(-1), dry weight) and HMs (As, 22,770-36,639 μg kg(-1); Cr, 39,333-133,343 μg kg(-1); Cu, 36,145-159,270 μg kg(-1); Pb, 51,210-166,642 μg kg(-1); Cd, 475.4-1,818.9 μg kg(-1); Hg, 59.9-460.8 μg kg(-1); and Se, 331.7-1,250.4 μg kg(-1), dry weight) were close to those obtained from other urbanized and industrialized areas, which have been considered moderately polluted. There was a clear positive correlation between MN potency and the molar concentrations of Hg and Pb in the sediments (Hg, r = 0.94; Pb, r = 0.91), suggesting that Hg and Pb were the most important factors that posed the sediments higher genotoxicity to V. faba root cells. Our results suggested that both biological and chemical approaches are necessary to be included in a battery of tests to assess the eco-environmental risks of sediments.