Molecular genetics deals with the genetic makeup of individuals which includes the identification and mapping of molecular genetic markers and genetic polymorphisms. Molecular genetic markers (DNA markers) are the powerful means for the genomic analysis and allow the connection of hereditary traits with genomic variation. Molecular techniques have led to the identification of multiple genes or markers associated with candidate genes that affect traits of interest in livestock, including genes for single-gene traits and QTL or genomic regions that affect quantitative traits. The discovery of genetic polymorphism at the DNA sequence level has been exploited as markers to explain the observed phenotypic variability in animals. Developments in molecular technologies like genomic selection may help overcome several of the limitations of traditional breeding programs and will be beneficial in breeding for lowly heritable disease traits that only manifest themselves following exposure to pathogens or environmental stressors. Application of molecular markers includes genetic diversity conservation, identification of disease carriers, parentage determination, marker-assisted selection, transgenesis, sex-determination and many more.The present review deals with the applications of molecular markers in versatile aspects that will prove beneficial to undertake further research to improve livestock health and production.