The conversion of exotic germplasm into domestic maize breeding materials is essential to solve the narrow genetic base for maize improvement in China. The present study applied SSR markers and three complementary cluster methods (STRUCTURE, UPGMA and PCoA) to 98 foreign hybridselected lines for effective hybrid breeding. A total of 450 alleles, with an average of 3.98 alleles per locus, were detected. Among 10 chromosomes, there were 13-19 loci and 33-59 alleles with averaged alleles 2.54~3.43 per chromosome. The polymorphism information content (PIC) among 10 chromosomes ranged from 0.4504~0.5582 and 69.4% PIC variation were explained by allele number/Locus. The highest PIC was observed in chromosome 7 (0.5582) and the lowest in chromosome 8 (0.4965). The STRUCTURE clustering analysis grouped the test lines into four subpopulations (i.e. REID, Lancaster, P and Domestic) in accordance with UPGMA and PCoA clustering. The higher genetic diversity were detected among the inbred lines in P and Domestic subpopulations. The allele frequencies, gene diversity and population structure obtained in the present study lead us to conclude that the 98 inbred lines derived from foreign hybrid-selected lines contain extensive genetic variation and are a valuable resource for Chinese maize breeding. The result obtained in the present study will assist in effective utilization of the lines in Chinese hybrid maize breeding programs.