Genetic diversity'refers to the variation of genes within a population or species, that is the combination of different genes found within a population of a single species, and the pattern of variation found within different populations of the same species. This covers distinct populations of the same species or genetic variation within a population. Ultimately, genetic diversity resides in changes in the sequence of the four base pairs of the DNA that constitutes the genetic code. Analyzing genetic variation with molecular technologies gives information at the DNA level. It can be neutral diversity, identified along the DNA sequence in regions whose function is unknown, such as when we use anonymous types of markers (e.g. AFLPs, RAPDs) or, the diversity can be based on known genes, that is, within the coding regions of the DNA sequence. This diversity affects the expression of those genes and, consequently, the RNAthe nucleic acid in charge of translating the information of the genetic code into proteins. Proteins, in their turn, are the elements that make up the structure of organisms, which means they are responsible for what we see, the phenotype. Hence, genotype and phenotype are closely associated. Phenotypic measures of diversity can also be used and, if correctly taken, they may reflect the molecular constitution of a given individual. Researcher must take into account that molecular tools can offer greater depth to diversity studies and that they provide a common groundfor measuring and analyzing diversity. However, molecular data are often complementary to other characterization data (e.g. morphology, pathology) and the combined analysis of these data may offer a more comprehensive ground for interpretation. Molecular markers have already played a major role in the genetic characterization and improvement of many crop species. They have also contributed to and greatly expanded our abilities to assess biodiversity, reconstruct accurate phylogenetic relationships, and understand the structure, evolution and interaction of plant and microbial populations. The first generation of molecular markers, RFLP, were based on DNA-DNA hybridization and were slow and expensive. The invention of the polymerase chain reaction (PCR) to amplify short segments of DNA gave rise to a second generation of faster and less expensive PCR-based markers. As technology grows new detection systems are developed in search for even more efficient marker systems and cost effective markers for the breeders of the 21st century for germplasm characterization and other uses. The TNAU is involved in the complete range of activities for the conservation and documentation of genetic resources in major cereals (rice, maize and ragi) and pulses (green gram, black gram and soy bean). This includes both domestic and foreign exploration, seed increase, characterization, evaluation, preservation, rejuvenation and documentation. Genomic tools will be employed maintenance and understanding to study the molecular diversity of these crops.