The wheat (Triticum aestivum L. and T. turgidum L.) stem rust resistance gene Sr6 confers a high level of resistance against a wide range of races of Puccinia graminis Pers.:Pers. f. sp. tritici Eriks. and E. Henn. in North America. In this study, we report the identification of flanking markers for Sr6. We used a population of 139 recombinant inbred lines from the cross MN99394 × MN98550. A partial linkage map of chromosome 2D comprised Xgwm484, Xcfd77, Xcfd43, Xwmc453, Sr6, XwPt_4381, XwPt_0330, Xgpw94049, and Xgwm102. Four markers mapped distal to Sr6, while the other four were proximal within distances of 4.8 and 6.5 cM, respectively. Marker-assisted selection and pyramiding of Sr6 with other stem rust resistance genes could benefit from the availability of Sr6- flanking markers.