The pomegranate (P. granatum L.) is a species belonging to the family Punicaceae. Pomegranate has high economic, nutritional, medicinal and ornamental value and has been cultivated more than two thousand years up to now and has developed quickly in recent years in our country. With the rapid development of molecular biology, based on DNA level, biomarkers have been widely applied. Therefore, first of all, some types of molecular markers which have been widely applied such as RFLP, RAPD, AFLP, SSR and ISSR markers, their principle and characteristics and their application in pomegranate are reviewed, and the existing problems are analyzed. Besides further deep-going and systematic research on the above aspects, it is suggested that in the future more attention should be paid to the application of molecular markers to pomegranate research in such aspects as molecular linkage map, marker-assisted selection breeding, germplasm valuation and identification, etc., which provide a scientific basis for the conservation of pomegranate germplasm resources, identification of genetic relationship and selective breeding of elite cultivars.