CRISPR/Cas9 system is a recently developed powerful technology for genome editing. The method has been successfully applied to genome editing in animals, and also to modify multiple target genes in plants over the past 2 years. But the editing efficiency of the system in Arabidopsis is much lower compared with that in rice, mainly due to the 35S-drived Cas9 has very low expression level in embryo sac by flower dip. In this study, the Cas9 gene was driven by the promoter of YAO gene, which is highly expressed in the embryo, embryo sac, endosperm and pollen. We introduced 35S:hSpCas9-BRI1-sgRNA and pYAO:hSpCas9-BRI1-sgRNA into the wild-type Arabidopsis to target BRI1 gene by Agrobacterium-mediated floral dip. pYAO:hSpCas9 generated a higher BRI1 mutation efficiency (90.5%) compared to 35S:hSpCas9 (4.3%) in Arabidopsis, and the T1 plants have more mutant alleles, some of them were heritable thought detection of Cas9-free T2 plants. PDS3 was selected to verify the system effect, the editing effiency could reach 88.5%.