Abstract: Marine microalgae were isolated from seawater and sediment samples collected from the intertidal zone of NaoZhou Island and Xuwen Coral Reef Nature Reserve, and identification and diversity of their strains with high contents of polysaccharides, lipids and proteins were analyzed by microalgal morphological observation, and sequence comparison and phylogeny analysis based on microalgal 18S rDNA sequences. A total of 189 strains of marine microalgae were isolated, cultured and identified, which represent 66 species distributed in 38 genera, 30 families, 25 orders, 9 classes, and belong to Bacillariophyta, Chlorophyta, Haptophyta and Rhodophyta of microalgae. Amongst, 46 strains with higher polysaccharide content belong to 25 species, and 20 genera, and 46 strains with higher lipid content represent 32 species belonging to 15 genera; and another 46 strains with higher protein content represent 28 species from 18 genera. It is concluded that the diversity of cultivable marine microalgae species and their strains with high content of polysaccharides, lipids and proteins is high from NaoZhou Island and Xuwen Coral Reef Nature Reserve, which possessed huge potential for exploring new drug or active natural products, functional food and fodder, and additives for food and fodder.