BackgroundSpecies of the genusMonascusare economically important and widely used in the production of food colorants and monacolin K. However, they have also been known to produce the mycotoxin citrinin. Currently, taxonomic knowledge of this species at the genome level is insufficient.MethodsThis study presents genomic similarity analyses through the analysis of the average nucleic acid identity of the genomic sequence and the whole genome alignment. Subsequently, the study constructed a pangenome ofMonascusby reannotating all the genomes and identifying a total of 9,539 orthologous gene families. Two phylogenetic trees were constructed based on 4,589 single copy orthologous protein sequences and all the 5,565 orthologous proteins, respectively. In addition, carbohydrate active enzymes, secretome, allergic proteins, as well as secondary metabolite gene clusters were compared among the included 15Monascusstrains.ResultsThe results clearly revealed a high homology betweenM. pilosusandM. ruber, and their distant relationship withM. purpureus. Accordingly, all the included 15Monascusstrains should be classified into two distinctly evolutionary clades, namely theM. purpureusclade and theM. pilosus-M. ruberclade. Moreover, gene ontology enrichment showed that theM. pilosus-M. ruberclade had more orthologous genes involved with environmental adaptation than theM. purpureusclade. Compared toAspergillus oryzae, all theMonascusspecies had a substantial gene loss of carbohydrate active enzymes. Potential allergenic and fungal virulence factor proteins were also found in the secretome ofMonascus. Furthermore, this study identified the pigment synthesis gene clusters present in all included genomes, but with multiple nonessential genes inserted in the gene cluster ofM. pilosusandM. rubercompared toM. purpureus. The citrinin gene cluster was found to be intact and highly conserved only amongM. purpureusgenomes. The monacolin K gene cluster was found only in the genomes ofM. pilosusandM. ruber, but the sequence was more conserved inM. ruber.ConclusionThis study provides a paradigm for phylogenetic analysis of the genusMonascus, and it is believed that this report will lead to a better understanding of these food microorganisms in terms of classification, metabolic differentiation, and safety.