The invention discloses a method, primer, probe and kit for identifying various gene mutations or substance genetic typing. In one embodiment, the disease is pathogenic. In the other embodiment, the invention is applied to detection of multidrug-resistant Mycobacterium tuberculosis, hepatitis B virus, beta-globulin mutation, thrombophilia related mutation; or various sexually transmitted pathogens, consisting of Trichomonas vaginalis, Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum, Treponema pallidum, Herpes simplex virus 1 , Herpes simplex virus 2, Human papillomavirus type 6, and Human papillomavirus type 1.