Abstract: The concept of utilizing markers in plant breeding as an indirect method of selecting desirable recombinant genotypes is well established. Until relatively recently, the markers employed were morphological characters which are limited in number and often agronomically undesirable. As a means of increasing the number of markers, different strategies have been developed based on existing natural variation present in plant genomes. The significance of this variation is that a large number of genetic markers can be assembled in a single cross. Further more, these markers are inherited in a Mendelian and hence, predictable manner. The availability of such markers provides new opportunities to improve the speed and precision of gene transfer in crop improvement. The suitability of different markers to be used to characterize the tissue culture plants has been reviewed in this paper. As the micropropagation industry is expanding somaclonal variation is becoming problems for the commercial propagator of a genotype. There is a severe need to have an effective reliable fast screening system to assure the genetic basis of the plants regenerated through tissue culture as a quality control measure.