Abstract: The F₂ population derived from crossing sorghum cultivars ‘B₂V₄’ and ‘1383-2’ was used as research material, with the SSR and MSAP markers used to detect the sorghum genome differences and construct methylation linkage groups. Results showed that the methylation linkage group LGC covered 44.3 cM, of which 23 loci were MSAP markers and three loci were SSR markers; the methylation linkage group LGD covered 46.2 cM, of which eight loci were MSAP markers and four loci were SSR markers. The methylation sites on linkage group LGC were from EcoRⅠ/MspⅠ enzyme digestion, but the methylation sites on linkage group LGD were from EcoRⅠ/MspⅠ and EcoRⅠ/HpaⅡ enzyme digestions. A dense methylation region near Xtxp 69 in LGC was identified. The MSAP marker rapidly detected genomic methylation differences and was able to construct a methylation linkage group in plants.