The invention provides a SNP molecular marker, a method, a primer composition, a kit and an application for identifying mycobacteria, and relates to the technical field of bacterial species identification. The SNP molecular marker contains a total of 17 SNP sites, which are distributed in the Hsp65 gene, rrs gene and pncA gene. Mycobacterium endogenous, Mycobacterium fortuitum, Mycobacterium kansasii, Mycobacterium gastric, Mycobacterium marinum, Mycobacterium microti, Mycobacterium scrofula, Mycobacterium smegmatis, Mycobacterium suja, Abscessus Polymorphisms in Mycobacterium, Mycobacterium ulcerans, Mycobacterium xenopus, Mycobacterium gordonii and Mycobacterium simiensis. The above primer composition can amplify Hsp65 gene, rrs gene and pncA gene, so as to be used for subsequent analysis of SNP molecular markers and identification of strains.