AFLP (amplified restriction fragment polymorphism) is an efficient molecular marker system for identification of varieties and genetic diversity research. Fifty-six improved wheat varieties released in Northwest Spring Wheat Region were analyzed by AFLP. Results of cluster analysis based on the AFLP data was basically consistent with the pedigrees of these varieties. At the same time, Correlation coefficient (r=0.86) between genetic distance matrices (Dice) based on the all AFLP bands and polymorphic bands indicated that all amplified bands should be included in order to realistically reflect the genetic relationship among varieties. However, for discrimination of varieties or capture of the accessions in core collections, we can only use the polymorphic band data. Multidimensional principal coordinate (PCO) analyses of these varieties based on the AFLP data showed that they can be clearly clustered into 5 groups, which is very helpful for further capturing these varieties. However, these varieties could not be clustered into groups clearly in the PCO figure based on the agronomic and botanic data, indicating the limitation of these data in revealing the genetic relationships among varieties. The low correlation coefficient (r=0.31) between the matrices based on agronomic and botanic data and AFLP data revealed the necessity to employ the molecular data in genetic diversity research and construction of a core collection.