Objective To explore the relationship between the genetic relationship and the cross compatibility of the wild rootstocks which belong to malus mill plants.Methods With the antecedent study in the cross compatibility of the rootstocks of malus mill plants, this paper focuses on the nrDNA ITS sequence analysis in the samples of the wild rootstocks which belong to malus mill plants from different 24 regions of China.Results It was successfully that having measured the sequence of 24 samples and having made the genetic distance matrix and genetic tree diagram.Conclusion There is a certain relationship between the genetic relationship and the cross compatibility of the wild rootstocks which belong to malus mill plants.