Nowadays, owing to the developments in molecular biology, genetic markers are generally used to describe specific regions of the genome. Three different marker systems, namely, protein and DNA markers, are used in genome analyses and in various genetic studies. Following the discovery of polymerase chain reaction (PCR), PCR-based marker systems are widely preferred in genetic studies. Genetic characterization studies are critically important to determine the level of genetic diversity between and within populations, origin of domestication and migration and development of conservation programs. Different biochemical marker systems, alloenzymes, mitochondrial DNA and Y chromosome are used for genetic characterization studies. DNA markers, especially the polymorphic microsatellite markers, are the most preferable marker systems in PCR applications. Recent progresses in molecular biology techniques allow rapid and economical identification of single nucleotide polymorphisms analyses and their applications along with microsatellites.