Combined with hairy root transformation,CRISPR/Cas9 is used to edit multiple sites in Nod factor receptor 1(NFR1) of Lotus japonicus and Glycine max, to quickly obtain the target mutants.The results showed that target gene mutants were generated in both of them. Editing efficiency of target 1 in LjNFR1 was 58.3%.No mutation was detected on target 2.The efficiency of target 1 and target 2 in Glycine max was 33.3% and 41.7%,respectively.Further sequencing analysis demonstrated that the CRISPR/Cas9 system is capable to simultaneously knockout multiple homologous genes in Glycine max,implying that the CRISPR/Cas9 can functionally manipulate redundant genes in plants.Exertion of the CRISPR/Cas9 system in transgenetic hairy roots shortened the experimental cycle of obtaining the desired mutants.