The genetic diversity of green-cotyledon black soybean cultivars native to Hebei province was evaluated based on ISSR and agronomic characters. The results indicated that 60 alleles of 7 ISSR markers were detected among 46 cultivars with an average of 8.57 alleles per ISSR marker, and the number of alleles per primer ranged from 5 to 17. The value of allelic polymorphism information content (PIC) ranged from 0.721 to 0.927, on the average of 0.82 per primer. The value of genetic similarity (GS) indices of 46 cultivars based on the 14 agronomic traits and ISSR data varied from 0.067 to 0.533 and 0.43 to 1.0 respectively, with an average of 0.284 and 0.704, indicating that the genetic diversity among green-cotyledon black soybean cultivars from Hebei is abundant. The clustering results showed that the groups could reflect the origin of the cultivars.