Two genes(RacGAP1 and RacGAP3) in Lotus japonicus were identified to explore the function of small GTPase activating protein during symbiotic process. Results of pulldown assay showed that both RacGAP1 and RacGAP3 are able to interact with ROP6 CA. The result of analyzing transcription showed that RacGAP1 and RacGAP3 were expressed mainly in vascular system of roots and downregulated expressed after being inoculated with Mesorhizobium loti. Promoters of the two genes were fused with GUS reporter and separately transferred into L. japonicus by hair roots transformation. The results showed that RacGAP3 was expressed in lateral root primordia and nodule primordia,but there was no expression of RacGAP1 in both primordia.RacGAP1 and RacGAP3 LORE1 insertion mutant didn’t show any defects about nodulation. However,homozygous plants of RacGAP1 exhibited severe defects in reproduction with withered flowers and fewer pods in comparison with the wildtype. It is indicated that RacGAP1 may be involved in flower development and RacGAP3 may negatively regulate the early symbiotic process in L. japonicus.