A data matrix, obtained during a 3-year monitoring period (2010-2012) from 45 sampling locations in the marine of Hong Kong, was subjected to pollution indicator and multivariate statistical technique analysis to investigate the spatial distribution and origin of the selected 12 heavy metals. Results suggested that V, Ni, and Ba were at safe levels, and there was a significant anthropogenic effect on Zn, Pb, Cu, Cd, and Cr, which were moderate to severe enrichment at some locations. Sampling locations 1, 2, 7, 9, 12, 13, 14, 30, 31, and 32 were identified as pollution hot spots. Principal component analysis and cluster analysis showed that Zn, Pb, Cu, Cd, and Cr were primarily controlled by anthropogenic sources and Ni, Ba, and V by natural sources. Whereas, Al, Fe, Mn, and As were controlled by both anthropogenic and natural sources. Cluster analysis classified 45 sampling sites into five groups and analysis of variance indicated there were significant differences between different groups. The pollution hot spots were classified into moderate or high polluted groups, and the influential factor of the heavy metal distribution was analyzed.