Molecular markers are defined as the fragments of DNA sequence associated with a genome, which areused to identify a particular DNA sequence. Nowadays, with the explosive growth of genetic research and bacterial classification, molecular marker is an important tool to identify bacterial species. Taking account to its significant roles in clinic, medicine and food industry, in this review article, we summa rize the traditional research and new development about molecular markers (also called genetic markers) in bacteria, including genes of 16S rRNA, 23S rRNA, rpoB, gyrB, dnaK, dsrAB, amoA, amoB, mip, horA, hitAM, recA, ica, frc. oxc, 16S-23S rDNA ISR and IS256.