Assessments of temporal change of marine biodiversity of coral reefs In Phu Quoc Marine Protected Area (MPA) were conducted at 10 permanent sites from 1994 to 2010 using SCUBA. The coral reefs in the MPA were not in good condition. Cover of hard corals heavily decreased over time, being highest in the period of 1994-2002 (mean: 20.0 percent) and 2009-2010 (21.2 percent) but this was stable in the period of 2002-2009. Coral reef resources increased at most of the study sites during 1994-2010, mainly by increasing of small fishes at size class of 1-10cm whereas the density of target fishes decreased or remained stable following years of study. Indicators of macro-invertebrates were extremely rare at all of study sites and the temporal change in density of these in dicators were not clear with an exception of decrease of sea urchins (Diadema spp.) in the period of 2009-2010. The notable decline in cover of hard corals may be explained by impacts of destructive fishing used in the period of 1994-2002 and of the bleaching event occurred in 2010. Generally, marine biodiversity of coral reefs in Phu Quoc MPA are still overharvested and have not been recovered, even in the protected zone after 4 years of management.