A major quantitative trait locus (QTL) controlling pod dehiscence (shattering) in soybean, designated qPDH1, has previously been identified using progeny of shattering-resistant cultivars derived from a Thai cultivar, SJ2. The QTL was located near a simple sequence repeat marker, Sat_366, on linkage group J. To determine whether shattering-resistance genes originating from different resources are located at qPDH1 in general, we conducted genetic analysis using DNA markers for several populations. In an F-2 Population derived from a cross between a shattering-susceptible cultivar, Toyomusume, and a shattering-resistant cultivar, Harosoy, a major QTL for pod dehiscence was identified in the region near qPDH1, which was confirmed in the progeny of F-4:5 populations. A major QTL was identified near qPDH1 also in F-2 populations derived from crosses including Wasekogane and Kariyutaka as shattering-resistant parents. The heterozygous genotypes at the QTL showed high degrees of pod dehiscence, suggesting that shattering resistance behaves as a nearly recessive trait. In F-2 Populations derived from crosses between shattering-resistant cultivars, heterozygous genotypes at the Sat_366 locus were shattering-resistant. These results suggest that shattering-resistant cultivars harbor recessive shattering-resistance allele(s) at qPDH1 regardless of their origin and that molecular markers near qPDH1 could be used for marker-assisted selection for shattering resistance in soybean.