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Genome sequencing has emerged as the leading discipline in the plant sciences coinciding with the start of the new century. For much of the twentieth century, plant geneticists were only successful in delineating putative chromosomal location, function, and changes in genes indirectly through the use of a number of “markers” physically linked to them. These included visible or morphological, cytological, protein, and molecular or DNA markers. Among them, the first DNA marker, the RFLPs, introduced a revolutionary change in plant genetics and breeding in the mid-1980s, mainly because of their infinite number and thus potential to cover maximum chromosomal regions, phenotypic neutrality, absence of epistasis, and codominant nature. An array of other hybridization-based markers, PCR-based markers, and markers based on both facilitated construction of genetic linkage maps, mapping of genes controlling simply inherited traits, and even gene clusters (QTLs) controlling polygenic traits in a large number of model and crop plants. During this period, a number of new mapping populations beyond F2 were utilized and a number of computer programs were developed for map construction, mapping of genes, and for mapping of polygenic clusters or QTLs. Molecular markers were also used in the studies of evolution and phylogenetic relationship, genetic diversity, DNA fingerprinting, and map-based cloning. Markers tightly linked to the genes were used in crop improvement employing the so-called marker-assisted selection. These strategies of molecular genetic mapping and molecular breeding made a spectacular impact during the last one and a half decades of the twentieth century. But still they remained “indirect” approaches for elucidation and utilization of plant genomes since much of the chromosomes remained unknown and the complete chemical depiction of them was yet to be unraveled. Physical mapping of genomes was the obvious consequence that facilitated the development of the “genomic resources” including BAC and YAC libraries to develop physical maps in some plant genomes. Subsequently, integrated genetic–physical maps were also developed in many plants. This led to the concept of structural genomics. Later on, emphasis was laid on EST and transcriptome analysis to decipher the function of the active gene sequences leading to another concept defined as functional genomics. The advent of techniques of bacteriophage gene and DNA sequencing in the 1970s was extended to facilitate sequencing of these genomic resources in the last decade of the twentieth century.