During the past three decades, the development of molecular genetics, especially DNA based markers has an important role in the field of animal genetics and breeding. Instead of conventional breeding program through selection alone, utilization of molecular genetic tools can ease us in optimizing the animal breeding program. Selection according to genotype has become an important tool in the breeding of farm animals. Molecular markers, revealing polymorphisms at the DNA level are the powerful tools to study the variation. These molecular markers have wide range of applications in population genetics, conservation biology and evolutionary biology. This review gives a brief summary on the characteristics of different molecular markers including hybridization and PCR-based markers.