The genome study of magnolia, which is one of tne basal angiosperm groups, will provide a key to understanding the origin of angiosperm and its diversifications. We determined the chloroplast whole genome of Magnolia kobus DC., a deciduous magnolia, using Solexa/Illumina technology without any additional gap filling. The chloroplast genome of Liriodendron tulififera, a previously sequenced taxon in the Magnoliaceae, is blasted against 168 million reads, and about 500X coverage of chloroplast genome sequences are recovered. A combination of assemblies by NGS CELL (ver. 3.1.0), ABySS, and VELVET generate the contigs which cover the entire region of the chloroplast genome. About 10 kbp (6.2%) of sequences are confirmed by the Sanger method, and the error rate was zero. The chloroplast genome of M. kobus is 159,245 bp long and has four subregions: 87,484 bp of large single copy and 18,595 bp of small single copy regions are separated by 26,583 bp of inverted repeat regions. There are 129 genes in the genome, of which 17 are duplicated in IR. The gene order of M. kobus is identical to those of two previously published chloroplast genomes in the family. Comparing M. kobus with M. kwangsinensis, which is an evergreen magnolia, the mean divergence rates of genes and intergenic spacers are 0.27% and 0.51%, respectively. Strikingly, we found 656 bp of long gap located between psbE and petL in M. kobus. The inverted repeat regions of two Magnolia species are three bp longer than L. tulififera. Future implications of this method in the studies of angiosperm phylogeny are also discussed.