In this paper, we characterized the Wx-mq gene for low amylose content in a rice variety, Milky Queen, at the molecular level. The Wx-mq gene was cloned by RT-PCR, and a nearly full-length cDNA sequence of the gene was determined. Sequence comparison between the Wx-mq gene and the wild type allele (Wx-b), cloned from cv. Koshihikari, revealed that two base changes existed within the coding region; a G to A base change at nucleotide position 497 and a T to C base change at nucleotide position 595. Each nucleotide substitution should generate a missense base change (an Arg-158 to His-158 change in exon4, and a Tyr-191 to His-191 change in exon5). However, it is not known which missense mutation is essential for the activity of the WX protein. To identify rice varieties and lines, which harbored the Wx-mq gene, PCR primers were designed at the gene level. These primers were able to amplify the Wx-mq specific 741 bp band in Milky Queen, and in other rice variety and lines, Milky Princess, Joiku 436 and Etsunan 190, all of which have the same pedigree as that of Milky Queen. On the other hand, no 741 bp band was amplified with the primers in Koshihikari which harbored the wild type allele (Wx-b), and the other low-amylose content variety and line, Snow Pearl and NM391, which do not have the pedigree. Thus, it is possible to detect the Wx-mq gene by PCR.