Molecular markers related to flour qualities of long spike wheat lines were evaluated. Ash, wet gluten and protein content of long spike wheat lines were higher than Keumkang(Korean wheat cv.) but SDS-sedimentation volume(SDSF) was lower. Particle size and lightness of flour of long spike wheat lines showed similar to Keumkang. The high positively correlation was presented between protein content and SDSF, wet gluten and particle size, respectively. However, negatively correlation was between protein content and lightness. Through the analysis of molecular markers, we identified the genotypes of four genes, Glu-A3c, Wx-A1a, Wx-B1a and Wx-D1a. These genes had same genotypes with Keumkang. Six genes, Glu-A1c, Glu-B1c, Glu-D1a, Glu-B3g, Pina-D1and Pinb-D1b, were presented in most of the lines. Two genes, Glu-A1 and Glu-B1b, were related to higher protein contents and wet gluten. The lines containing three genotypes, Glu-D1d, Glu-B3h and Pinb-D1b, had higher ash, protein contents, SDSF and wet gluten, and lightness was darker. Through the results, we expect that long spike type wheat lines are necessary to breed wheat having high yield productivity.