Microsatellites or Simple Sequence Repeats (SSR) have been preferred molecular markers ever since their advent in the late eighties. SSR are tandem repeat units of 1 to 6 base pair that are found in many prokaryotic and eukaryotic genomes. Despite growing rivalry from new sequencing and genotyping techniques, the use of these mobile and efficient markers continues to increase, boosted by consecutive technical advances. Random determined expansions look to be elite against for at least part of microsatellite loci, probably because of their effect on organization of chromatin, gene regulation, recombination, replication of DNA, cell-division cycle, mismatch repair system, etc. The illustration methods used previously for finding new microsatellite loci in sand files remain difficult and time consuming; insilico approach, which includes retrieval and investigation of microsatellites from large amounts of sequence data from sequence data based using microsatellite tools can yield many new candidate markers. To make the most of the latest technical developments and outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatics tools, from primer design to allele calling. In this review also cover the role of microsatellites in identification and isolation of genotypes, characterization and analysis of genetic diversity, and their interactions in SSR variation.