Visual censuses of coral reef fishes in Nha Trang Bay Marine Protected Area (MPA) were conducted during September–October 2005. Nha Trang Bay MPA is relatively rich in reef fishes compared to other areas in Vietnam and the Pacific Ocean outside the ‘Coral Triangle,’ consistent with its biogeographic location in the western South China Sea. A total of 266 species of 40 families of coral reef fishes formed five distinct assemblages. Spatial variations in distribution and structure of the assemblages were associated with eight significant biological and physical variables which were cover of living hard corals, encrusting corals, branching corals, Acropora, Millepora, Montipora, depth and distance from the coast of the mainland. The six factors in front are likely related to provision of shelter and nutrition, while the distance factor is likely to represent a gradient in disturbance and impacts from various mainland sources including sedimentation and pollution discharge from nearby rivers. Local species richness ranged from 35 to 70 species 500 m−2 (mean: 51 ± 2 SE) for reef flat stations and from 23 to 68 species 500 m−2 (mean: 48 ± 4 SE) for reef slope stations. Total species richness at each site averaged 76 species (±4 SE), ranging from 56 to 110 species, dominated by wrasses, damselfishes, butterflyfishes, parrotfishes, surgeonfishes, groupers and goatfishes. Density of total fishes at each station ranged from 348 to 1,444 individuals 500 m−2 (mean: 722 ± 302 SE) for the reef flat stations and from 252 to 929 individuals 500 m−2 (mean: 536 ± 215.7 SE) for the reef slope stations. Overall mean density at each site averaged 628.9 (±238.4 SE) individuals 500 m−2. The highly protected sites supported higher mean density of fishes per site (ranged: 904.5–1,213 individuals 500 m−2 for Hon Mun and 1,167.5 individuals 500 m−2 for Hon Cau) compared to other sites (<800 individuals 500 m−2). Of the families included in the census, densities were dominated throughout the MPA by damselfishes and wrasses. Many target species, particularly groupers, snappers and emperors, were rare or absent and the low abundance of big fishes was consistent with over-harvesting. Similarly a low density of butterfly fishes and angelfishes is likely related to the supply for marine aquaria in Vietnam and overseas. This study provides an important baseline against which the success of present and future MPA management initiatives may be assessed.