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Foxtail millet (Setaria italica), which originated in China, is an important crop with high genetic diversity. In recent years, several cultivars were developed, but parental cultivars resources are still limited. Inter-simple sequence repeat (ISSR) markers can be used with a high degree of automation and are advantageous tools for genetic diversity analysis. The objective of this study was to analyze genetic diversity in 30 cultivars of foxtail millet using the fluorescent ISSR technique. Eight ISSR markers were used to analyze the genetic diversity in 13 cultivars in Shanxi (SX), 7 in Hebei (HE), 4 in Inner Mongolia (IM), 2 in Shaanxi (SN), 2 in Henan (HA) and 2 in Liaoning (LN), respectively. A total of 122 bands, of which 105(84.5%) were polymorphism bands, were obtained. The average number of polymorphic information content (PIC), marker index (MI) and resolving power (RP) of eight ISSR primers in this study was 0.9, 12.04 and 5.54, respectively. Nei's genetic distance varied from 0.56 to 0.93. Cluster analysis classified the 30 cultivars into three groups. The cultivars from SX province could be placed together in Group II, but SN, HE and IM were placed in Group I. Group III contained germplasms from different regions (SX, HE, HA and IM), In conclusion, our results indicate high genetic diversity among 30 Chinese foxtail millet cultivars, which could contribute to future breeding programs and functional genomic research. [ABSTRACT FROM AUTHOR]