Radish (Raphanus sativus L.; 2n=18) is an important vegetable grown around the world, and is one of the major root crops in East Asia. In Japan, more than 700 radish cultivars called ’Daikon’, which means large root, have been established. These cultivars show remarkable morphological and physiological variation in the shape, size, color, and contained materials in the roots. Despite the agricultural importance and biological uniqueness, the genomic and the molecular genetic studies of radish have been limited. Our genome project aims to firstly determine a draft genome sequence of cultivated radish (the genome size is approximately 570Mb). Using next-generation sequencing technology, we conduct de novo genome assembly, map contigs and scaffolds to the genetic linkage map of nine pseudochromosomes, and predict gene models. Comparative genomic studies among radish, the Brassica species that are close relatives of radish, and Arabidopsis will contribute to elucidate the structural differences of the crucifer genomes, genomic signature of bottlenecks in radish breedings, roles of genome duplication and rearrangements in functional evolution of some important agronomic traits. In addition, we conduct comprehensive sequencing of cDNA libraries sampled from various organs and tissues in several developmental stages. The transcriptome analysis will contribute to address genetic backgrounds of root morphogenesis and promote breeding programs of radish.