Abstract: This research was made in three coral reef of Colima State, México (La Boquita, Club de Yates and Punta Carrizales) which are treated by coastal development, marine pollution and human smugglers of ornate fish. The main goal was to obtain species richness, estimation of fish relative abundance and others ecological indices of reef fish assemblages in order to provide baseline to future changes. The fish census was obtained through underwater observation during the year 2004. A total of 4,627 organisms were recorded in a surface area of 3,100 square meter of the three selected areas. Forty six species belonging to 23-families were detected. Most species-rich families were Pomacentridae (5 species) followed by Lutjanidae and Labridae (4 species) and Acanthuridae, Carangidae, Haemulidae (3 species). Of this species recorded in La Boquita most abundant were Thalassoma lucasanum (30%), 22% belongs to Stegastes acapulcoensis and 19% to Chromis atrilobata. In Carrizales the most abundance species belongs to Haemulon maculicauda with 14.8% and Stegastes acapulcoensis with 18% By last, Club de Yates, 17% belong to Prionurus punctatus and Haemulon maculicauda with 14%. The density organism per square meter was higher in the Club de Yates with 1.8 organisms, Carrizales with 1.5 and minor in La Boquita with 1.26 organisms. The values of diversity index and equity also were estimated. They fluctuate between 0.84 in La Boquita and 0.94 in Club de Yates. These results indicate changes of reef fish assemblages between sites in the littoral of Colima derive by physical and biological factors. It is important to take conservation measurement to protect this ecosystem in Colima.