The Kingdom Fungi is being studied extensively across the globe due to their beneficial role in diverse fields namely medicine, fermentation, food industry, bioremediation, biofertilizers and biopesticides. It is also true that most of the plant diseases are caused by fungi, resulting in heavy losses in the crop yield. Fungi vary in size from single cell to multi cell and divergent group of fungi is composed of yeasts, molds, mushrooms, lichens, disease causing rusts and smuts. Due to increase in population worldwide and depleting environment, man is trying to find novel advanced techniques to meet the population demands; and this purpose was resolved through the advancements in molecular biology, which is being utilized in every aspect of biological science. Over the past five decades, advancements in the field of molecular biology has opened up a new array of
diagnostic tools to the researchers for addressing issues from gene expression to genetic diversity. The ready availability of DNA sequence data has led to major developments in the study of the biochemistry, ecology, strain characterization, identification, pathogen detection, genomics, molecular diagnosis of fungi, and association with other organisms (Bruns et al., 1991). A molecular marker is a short fragment of DNA that is associated with certain gene in the genome or the marker that reveal variations at DNA level. The first DNA based molecular marker developed is restriction fragment length polymorphism (RFLP) by Grodzicker et al. (1974).