This paper presents the results of a 6-year (1998–2003) survey of trace toxics in the intertidal mussel Perna viridis conducted by the Hong Kong Environmental Protection Department. Concentrations of heavy metals and trace organics were measured in the soft bodies of P. viridis collected from five sites in Hong Kong waters, i.e. Wu Kai Sha (Tolo Harbour), Ma Wan (Northwest), Tsim Sha Tsui (Victoria Harbour), Tai Tam (Hong Kong South) and Lamma Island (Southern Waters) in order to establish the spatial patterns of contaminants in mussels. Among the metals analysed, Cd showed a significant concentration gradient in Hong Kong waters. The levels of Cd in P. viridis were significantly higher at Ma Wan as compared to the other sites studied. Ma Wan also had relatively higher concentrations of Pb. Mn concentrations were particularly prominent at Wu Kai Sha. Significantly higher concentrations of Hg and Cu were recorded at Tai Tam and Tsim Sha Tsui. Tai Tam and Wu Kai Sha had higher levels of V; whereas higher Ni concentrations were recorded at Lamma Island and Tai Tam. No clear spatial patterns for Al, As, Cr, Fe and Zn were observed. Higher concentrations of PAHs in P. viridis were observed around urban centres impacted by sewage discharges (e.g. Tsim Sha Tsui); whereas higher PCB levels were found not only in Tsim Sha Tsui but also in less urbanised areas such as Lamma Island and Tai Tam, suggesting that these may be due to non-sewage related inputs. The study also shows that Northwest and Southern waters are subject to a higher degree of DDT pollution compared with other sites. Of the 17 dioxin compounds analysed, positive data were mostly recorded for two compounds which are of low toxicity (i.e. OCDD and 1,2,3,4,6,7,8-HpCDD) whereas the most toxic congeners (i.e. 2,3,7,8-TCDD and 1,2,3,7,8-PeCDD) were not detected in the 6 years of monitoring. In general, the levels of OCDD in P. viridis were found to be higher in Tai Tam and Lamma Island in Southern Waters of Hong Kong. This study found that the levels of some highly toxic heavy metals (i.e. Cd, Hg and Pb) in the mussel P. viridis did not exceed the recommended limits for shellfish as food in Hong Kong (i.e. Cd: 2.0 ppm; Hg: 0.5 ppm; Pb: 6.0 ppm wet weight). The levels of As and Ni in P. viridis were also well below the action limits set by the US FDA (i.e. As: 86 ppm; Ni: 80 ppm wet weight). DDT and PCB contaminations in P. viridis were below the concentrations of concern. Compared with data obtained in the 1980s, the current levels of DDTs in P. viridis were 4–16 times lower; whereas Pb concentrations recorded in Tsim Sha Tsui have also been lowered significantly. This is mainly related to reduction in local and regional pollution sources in the past 20 years.