Abstract: The capillary electrophoresis is used for detecting the polymorphisms among 34 Nanzhao Magnoliae Flos (MF) lines amplified by SRAP primers. The genetic similarity coefficient and cluster analysis and DNA fingerprints are conducted, providing the theoretical basis for variety identification and molecular breeding. The results show that: (1) A total of 71 bands are amplified from 34 Nanzhao MF lines using five pairs of SRAP primers, among which 59 demonstrated polymorphisms (83.1%). Each pair of SRAP primer amplified 9~15 polymorphic bands, with an average of 11.8. (2) Based on the two pairs of primers with high polymorphism and strong discriminating ability, DNA fingerprints of 34 Nanzhao MF based on 22 loci are constructed. (3) The genetic similarity coefficient is between 0.58~0.97. UPGMA clustering results show that those lines can be classified into six groups, and there is no direct relationship between the groups and sample locations.