Most of the crop plants have large and complex genomes. Maize and wheat genomes have a size of 2300 Mb and 16500 Mb respectively. Until recently the sequencing of these complex genomes was considered intractable. But now the genome sequencing technology is undergoing a revolution with the commercialization of second generation technologies capable of sequencing millions of bases in a single run. In the coming years these technologies will further add to the available information regarding the genomes. The second generation sequencing technologies have already been commercialized and the third generations sequencing strategies will be available soon in the near future. Within no time the toughest genomes like that of wheat will be available for utilization in crop improvement. The resulting information about the genes and molecular markers will revolutionize the crop breeding program if this information is applied to our advanced genotyping methodologies.