Prometaphase chromosomes of Coix lacryma-jobi L. were quantitatively analyzed based on their distribution patterns of DAPI signals. The DAPI signals showed prominent uneven distribution along the chromosomes. Based on the DAPI signal patterns, a quantitative chromosome map was constructed for the first time in C. lacryma-jobi. The quantitative chromosome map will offer the foundation for genome analysis of C. lacryma-jobi.