Chilling temperatures (similar to 15 degrees C) at flowering cause a brown pigmentation in the seed coats of soybean (Glycine max (L.) Merr.) around the hilum region. It has unfavorable effects in confectionary uses. The degree of pigmentation due to chilling was strongly dependent on developmental stages of flowers and increased with the age of flowers at the time of chilling treatment. Genetic analysis was performed using F-1 hybrids and F-2 population derived from a cross of a sensitive cv. Kitakomachi and a tolerant cv. Koganejiro in order to determine the genetic basis of pigmentation. Analysis of F-1 hybrids showed that the sensitivity was incompletely dominant to the tolerance. In F-2 progeny, degree of pigmentation varied continuously with a skew to Kitakomachi. The minimum number of genes concerned was estimated to be 1.25 by the method of Castle-Wright and 1 by the maximum likelihood method. Therefore, one or two major genes were involved in the pigmentation. Linkage analysis with six marker genes indicated that one of the genes responsible for the pigmentation is linked with a maturity gene for insensitivity to incandescent long daylength. Selection for delayed maturity in segregating populations may be an indirect but effective method to improve the chilling tolerance. Five marker genes, Ln, Enp, ldh2, Ti, and Acol, segregated independently with genes for the pigmentation.