MPA (Mycobacteriaceae Phenome Atlas) is a Mycobacteriaceae phenome database, which integrates the phenomic data of Mycobacteriaceae strains by literature mining, third-party database integration, and bioinformatics annotation. The phenotypes of Mycobacteriaceae are inferred from available phenomic data, and 82 microbial phenotypic traits were recruited as data elements of the microbial phenome, containing 5 categories and 20 subcategories of polyphasic phenotypes, and 3 categories and 8 subcategories of functional phenotypes, all of which are complementary to the existing data standards of microbial phenotypes. The phenotypes were searchable and comparable from the website of MPA. A network analysis of MPA topological data revealed the co-evolution between Mycobacterium tuberculosis and some important phenotypes, such as virulence factors, and also uncovered potential pathogenicity-associated phenotypes. The application of MPA may provide novel insights into the pathogenicity mechanism of Mycobacteriaceae.