Microsatellites or SSRs (Simple Sequence Repeats) are characterized as short sequences, which are 1 to 5 bp long. These monomer units display tandem organization representing hypervariable loci where the variations arise due to the differences in the number of repeating units forming the repeat array. ISSR technique allow the detection of SSR derived polymorphisms directly from the genomes without the need to isolate and characterize these sequences. These are single primer PCR reactions in which exponential amplification takes place only when the particular repeat used as a primer is represented in multiple copies which are closely spaced (<2-3kb) and inversely oriented in the template DNA. SSR based primers representing di- tri- tetra- and penta- nucleotide repeats can be successfully used to generate distinct banding patterns that are resovable on low resloution agarose gels using ethidium bromide staining.

ISSRs are subjected to irreproducibility effects as they are very sensitive to the reaction conditions and also, the SSR-based primer can anneal in many possible positions at each target site, resulting in multiple heterogenous products from each locus. An addition of a non-repeat base at the 3' or 5' end of SSR based primer, anchors the primers to a specific target in the genome in such a manner that every new amplification reaction begins essentially from the same site. The compound microsatellite primers can also be used for anchorage and will detect polymorphism only when two SSRs are present in tandem. Anchoring of primers at the 5' end results in the inclusion of the entire SSR sequence in the amplification product with a higher probability in comparison to 3' anchored primers.