The invention provides an SNP molecular marker and method for identifying mycobacteria, a primer composition, a kit and application, and relates to the technical field of strain identification. The SNP molecular marker comprises seventeen SNP loca distributed in an Hsp65 gene, an rrs gene and a pncA gene, and when marked in mycobacterium tuberculosis, mycobacterium bovis, Africa mycobacterium, mycobacterium avium, intracellular mycobacterium, mycobacterium fortuitum, mycobacterium kansasii, mycobacterium gastri, mycobacterium marinum,volemycobacterium, mycobacterium scrofulaceum, mycobacteriumsmegmatis, suga mycobacterium, mycobacterium abscessus, mycobacterium ulcerans, toad mycobacterium, mycobacterium gordonae and ape mycobacterium, the SNP molecular marker has polymorphism. The primercomposition can amplify the Hsp65 gene, therrs gene and thepncA gene to be used for analyzing of the SNP molecular marker and strain identification.