ABSTRACT.A combination of phenotypic characterization and molecular markers may provide reliable information on new plant varieties and elucidate the conservation status of rare species. Five newly developed Magnolia wufengensis cultivars, an endangered plant species endemic to Hubei Province, China, possess more distinctive phenotypes than common Magnolia cultivars. With reference to a wild species population of M. wufengensis and a population of Magnolia denudata, morphological traits of flower organs, simple sequence repeat (SSR), and sequence-related amplified polymorphism (SRAP) markers were used. In the morphological study, six traits of floral organs were investigated and their relationships were analyzed between cultivars. In the genetic study, 9 SSR primer pairs and 10 SRAP primer combinations were screened. The five cultivars maintained a high level of genetic diversity. Genetic diversity of each M. wufengensis cultivar was much lower than that of the wild population, but was slightly higher than that of the M. denudata population. Analysis of molecular variance (AMOVA) revealed that genetic variation among populations was 20% (SRAP) and 30% (SSR), which showed a high degree of genetic differentiation among populations of the five cultivars. The dendrograms illustrated a clear separation between M. wufengensis populations and outer species, and identified two major groups among cultivars. Correlation analysis indicated a good fit between the two marker systems, but a relatively low fit between morphological and genetic traits (SRAP: r = 0.60, SSR: r = 0.52). These findings provide reliable references for the application of these molecular markers in the breeding and conservation of M. wufengensis.