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A total of 192 native rice germplasm lines from the cold region of Northeast China were analyzed for rice sheath blight resistance at the late tillering stage using the toothpick embedding method. Disease rating, absolute disease lesion height, relative lesion length and lesion length served as indicators of sheath blight resistance. Germplasm resources were then subjected to population structure analysis and linkage disequilibrium analysis in order to identify disease resistance markers for use in marker-assisted breeding for sheath blight resistance. The germplasm resources were segregated into three main groups .Notably, a total of nine markers were significantly associated with rice sheath blight resistance; eight of these markers(OSR23, RM270, RM339, RM470, RM536, RM569,RM1022, RM1163) were associated with disease rating. The additional marker RM283 was associated with both relative lesion length and lesion length and made a high contribution to the rate of phenotypic variation. Ultimately, the sheath blight resistance markers described in this study could be useful for rice marker-assisted selection of sheath blight resistant cultivars breeding.