To study the relationship between main phenotypic traits and yield and quality of Isatis indigotica gemplasm,with 31 different sources of I.indigotica germplasms as materials,cluster analysis of 16 phenotypic traits and correlation analysis of 10 main quantitative traits were conducted,and quality traits concentrations of uridine,guanosine,adenosine and (R,S)-gaoyichun in root were determined.It showed that the variance of the phenotypic traits in 31 I.indigotica germplasms was abundant and they could be divided into three categories at 10.0 of the European distance.The fresh root mass showed an outstanding positive linear correlation with fresh leaf mass and root diameter,the fresh leaf mass showed an outstanding positive linear correlation with leaf number per plant,leaf length and width(P<0.01),so root yield of I.indigotica could be improved by increasing the fresh leaf mass,leaf yield could be improved by increasing leaf length,leaf width and number of leaves per plant.It also showed that there was no direct relationship between phenotypic traits of I.indigotica and quality traits concentration of uridine,guanosine,adenosine and (R,S)-gaoyichun in root.In a word,the genetic relationship of I.indigotica germplasms can be known by cluster analysis of phenotypic traits in different I.indigotica germplasms.The yield of Folium isatidis or Radix isatidis can be increased by selective improvement of the leaf number per plant,leaf size,or root diameter.