SRAP molecular marker was used to detect the genetic diversity of 24 mulberry genotypes in the lower regions of the Yellow River in order to analyze the genetic relationships and pedigrees in the genus Morus L. Out of 88 PCR fragments scored, 69 (78.41 %) were polymorphic, with an average of 6.9 polymorphic bands and 8.0 bands per SRAP primer combination. A high degree of polymorphism was revealed by these combinations that ranged from 66.7 to 100 % across all the accessions studied. The genetic similarity coefficients among 24 local cultivars were relatively high with a range of 0.623–0.978. Both species of M. alba and M. multicaulis presented the abundant variations. As out-group, M. mongolica and M. bombycis were separated in the clustering tree, and other genotypes were divided into four groups. Clustering of some accessions of M. alba and M. multicaulis into strictly separate species was not readily apparent, in spite of their different geographic origin. The materials of M. alba and M. multicaulis were tangled in the different groups on dendrogram, which revealed that they have relatively close genetic relationships. High degree of cross-species reproductive success was encountered often in mulberry breeding programme, which caused the complex genetic background. Some accessions were proved to be inter-specific hybrid progenies by SRAP genetic information. Additional phylogenetic studies using cytoplasmic gene sequences would be helpful to further evaluate the systematic positions of these species or new established genotypes.