Recent molecular phylogenetic studies of Magnoliaceae based on the combined analyses of several cp DNA and nuclear DNA regions clearly showed eleven sublineages in the family. However, the relationships among these sublineages are still unclear because of low divergence rates in the family. It seems that Magnoliaceae diverged into several sublineages during a short period of time and more data is needed to get completely resolved phylogenetic tree. We determined eight chloroplast genomes representing each sublineage of Magnoliaceae using new generation sequencing (NGS) technology as well as the conventional PCR method. The mean divergence rate of entire regions from eight available cp DNA genomes in the family is only 1.00%. The phylogenetic tree based on eight whole genome data sets give resolutions to the polytomies found in the trees of previous studies. For example, a node of polytomy for M. kobus, M. sprengeri, and M. denudata in the previous phylogenetic studies has resolved in our result: M. kobus is a sister to M. sprengeri with 90% of bootstrap support. Fully resolved phylogenetic tree and re-evaluation of morphological characters based on it will give us an evidence for new classification system of Magnoliaceae.