With the advancements made in plant tissue culture techniques, it has now become possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerated plants. The occurrence of subtle somaclonal variation is a drawback for both in vitro cloning as well as germplasm preservation. Therefore, it is of immense significance to assure the genetic uniformity of in vitro raised plants at an early stage. Several strategies have been followed to ascertain the genetic fidelity of the in vitro raised progenies comprising morphophysiological, biochemical and cytological approaches. However, each tool has its own merits and limitations. These approaches are mainly based on characters, which can be affected by the in vitro manipulation, environment and types of plant tissue; hence it is no easy to differentiate clonal fidelity with a high probability. Presently, DNAbased molecular markers have acted as versatile tools in various fields of biology. Application of such DNA-based markers offers several advantages over traditional aforementioned markers, as they provide data that can be analysed objectively. In the present paper, strategies to ascertain and confirm genetic fidelity in a variety of in vitro raised plantlets are reviewed.