Microsatellites are tandemly repetitive DNA sequences with very short nucleotide motif (1-6bp) and their repeat arrays are generally no longer than 300bp. Genomes are scattered with simple repeats. Tandem repeats occur in the form of iterations of repeat units of almost anything from a single base pair to thousands of base pairs. Mono-, di-, tri and tetra nucleotide repeats are the main types of microsatellite, but repeats of five (penta-) or six (hexa-) nucleotides are usually classified as microsatellites as well.

SSR or microsatellites have been developed into one of the most popular classes of genetic markers because of their high reproducibility, Multi-allelic nature, Co-dominant mode of inheritance, abundance and wide genome coverage. Its use for integrating genetic maps, physical mapping, and anchoring gives geneticists and plant breeders a pathway to link genotype and phenotype variations.

High mutability at microsatellite loci has a role in genome evolution by creating genetic variation within a gene pool. This genetic variation occurs primarily by slipped-strand mispairing and subsequent error(s) during DNA replication or repair or recombination. Other possible factors such as the interplay of the repeat type, the genomic position of the microsatellite and the genetic-biochemical background of the cell are thought to contribute to the observed divergence of microsatellite distribution in different organisms. SSR assessments in the human genome have shown that many diseases are caused by mutation in these sequences. Then play an important role in gene regulation, pathogenesis, and bacterial adaptation and in evolution of genome. They also applied in various fields such as DNA fingerprinting, Paternity studies, forensics, Evolution Studies.ect.