Pythium stalk rot is a serious disease that threats the maize production. Exploration of the resistance maize germplasm resources to this disease will benefit for noval genes mining and the determination of heterosis patterns. Within this study, fourteen molecular markers linked to eight stalk rot resistance genes were used for genotyping 196 resistant maize germplasm accessions. Moreover, 42 polymorphic SSR makers were adopted in genetic diversity analysis of 54 selected resistant maize lines. A total of 128 resistance marker genotypes were identified with the eight functional markers. Out of 196 accessions, 191 exhibited one or more of fragments being identical with these of Qi319, X178 or 1145. No fragments were detected in five germplasm accessions (Yue61, Zheng653, Chi L136, Bai53, and 18--14), suggsting that these five germplasm might harbor other maize stalk rot resistance gene(s). By deployment of 42 SSR primers, 119 alleles were amplified in 54 selected lines, with polymorphic site percentage (PPB) of 99.17%. The average number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity (H), and Shannon’s information index (I) were 2.86, 1.7070, 0.3999, and 0.5884, respectively. The value of polymorphism information content (PIC) for each marker varied from 0.2061 to 0.7844, with an average of 0.5527. The UPGMA analysis classified 54 inbred lines into 2 groups and 6 subgroups with relatively high genetic diversity, including Lüda red cob (LRC), BSSS, Tang si ping tou (TSPT), PA, PB and Lancaster. Taken together, the results revealed variable resources with resistance to stalk rot in six heterosis groups, among which the most resistance germplasms were found in PA subgroup.