Objective Based on the sequence-related amplification polymorphism (SRAP) technology and the sequence similarity of internal transcribed space(ITS),β-tubulin and combined with morphological identification method, the phylogenetic relationships of different species of Monascus were inferred and a reliable method for rapid and accurate identification of Monascus was developed. Methods Using the Monascus genome as template, ITS and partial β-tubulin gene sequence were amplified and sequenced.Phylogenetic tree was constructed by using the maximum likelihood method with Mega 7.0 software. SRAP specific binding sequences were also amplified and the phylogenetic tree was built by using unweighted pair-group method with arithmetic means(UPGMA) algorithm with FigTree software in R phangorn package. A rapid and reliable identification method was built by analyzing the phylogenetic relationships of different species of Monascus. Results Combined with phenotypic analysis and two molecular identification method,16 strains of Monascus was identified as Monascus anka, Monascus aurantiacus and Monascus purpureus. Conclusion SRAP identification method had more detailed classification basis and could identify Monascus species quickly and accurately when combined with phenotypic analysis.