83 pairs of SSR molecular markers were used to analyze the genetic diversity of 81A. lancea materials and 5 Atractylodes macrocephala in different regions of Hubei Province and to construct DNA fingerprints. At the same time,the phenotypic data and medicinal quality of 86 materials were investigated,and chemical fingerprints were constructed. The results showed that a total of 420 loci were amplified by 83 pairs of SSR primers,and the number of polymorphic loci accounted for 97.14%. The genetic distance of cluster analysis based on SSR molecular markers was 0.63（A. lancea and A. macrocephala can be completely separated）. The genetic analysis of the population structure of different populations of materials revealed that the genetic variation originated from within the population,not between the populations. The correlation analysis and cluster analysis of the phenotypic data and the medicinal quality data of the materials tested found that there was a significant positive correlation (P<0.05) between the length of the bottom 4 leaves and the width of the bottom 4 leaves,the culm color,the culm diameter,the plant height,between the depth of leaf cracks and the number of branches in the upper part,between the culm color and the culm shape,and between the culm diameter and the number of branches in the upper part. There was a significant negative correlation between the culm shape and the number of branches in the lower part. The Q value (ratio of oil area and total root area) was significantly negatively correlated with the content of atractylodine. The content of β-eucalyptus was significantly positively correlated with the content of ether extract. The similarity of fingerprints of the materials tested was 0.80-1.00,and the similarity of Atractylodes macrocephala and Atractylodes macrocephala reached 0.89 through comparing the similarity of HPLC chemical fingerprint and analyzing the cluster of shared peak areas after quantification. It is indicated that the genetic background of A. lancea and A. macrocephalaare quite different,and the genetic basis of A. lancea is more complicated than that of A. macrocephala. There are big differences between the two active ingredients,but the difference between A. macrocephala materials is relatively small. Two different varieties of A. lanceaand A. macrocephala can be distinguished from the genetic level. It will provide a theoretical basis for screening and identifying A. lanceolata cultivars with high yield,high quality,disease resistant and high active ingredients.