Mulberry (Morus spp.) is an economically important tree crop being cultivated in India, China and other sericulturally important countries for its foliage to feed the silk producing insect Bombyx mori L. Genetic improvements of mulberry lag behind to the same in many other economically less important crops due to the complexity of its genetics, the breeding behavior, and the lack of basic information on factors governing important agronomic traits. In this review, the general usage and advantages of different molecular markers including isoenzymes, RFLPs, RAPDs, ISSRs, SSRs, AFLPs and SNPs are described to enlighten their applicability in mulberry genetic improvement programs. Application of DNA markers in germplasm characterization, construction of genetic linkage maps, QTL identification and in marker-assisted selection was also described along with its present status and future prospects.