The genetic diversity of 59 maize inbred lines and one teosinte accession was analyzed by using ISSR markers. With 21 ISSR primers, totally 475 alleles were detected among which 469 were polymorphic, and the average number of alleles for one primer was 22.6. Polymorphic information content (PIC) ranged from 0.84 to 0.94. The similarity coefficient of 60 accessions ranged from 0.23 to 0.48. Cluster analysis based on ISSR data showed that the accessions could be categorized into two groups and further 9 sub-groups,to some extent in accordance with the pedigrees of the entries and with some exceptions. Therefore, the present study indicated that ISSR marker was not the best marker system for assessment of genetic diversity although it might reveal genetic relationships among accessions. It was suggested that ISSR be used for assessment of genetic diversity in under-researched or neglected crops.