Aim The aim of this study was to screen potential lotus plant endophytic bacterial isolate for effective inhibition against lotus rot causing fungal pathogen Fusarium oxysporum. Methods and Results In this study, endophytic bacteria were isolated from lotus tissues and tested for antagonistic activities against the pathogenic fungus F. oxysporum. Among the putative endophytic Bacillus strains identified, suspensions of the strain B-36 showed the highest inhibition rate against F. oxysporum growth. Pot assays indicated that B-36 was effective in controlling F. oxysporum-inducing lotus rot. However, the control efficiency varied with the inoculation method and concentration, where injection of 800 mu l B-36 suspension per plant (2 x 10(8) CFU per ml) into stems showed the highest control efficiencies of 77 center dot 1 and 60 center dot 0% for pre-inoculation and post-inoculation. In addition, the colonizing population levels (CPLs) of B-36 on lotus also varied with the inoculation method and concentration, with the highest CPLs, that is, 3 center dot 05 and 2 center dot 83 log(CFU per gram), being observed on lotus leaves and stems respectively for stem injection of 200 mu l per plant. Moreover B-36 showed no noticeable effects on lotus seed germination rate or seedling growth. Finally, B-36 was characterized as Bacillus velezensis based on its morphology, Gram-positive characteristics, as well as its 16S rDNA and gyrB sequences. Conclusion The isolate B-36 can be applied as a biocontrol agent against F. oxysporum-inducing lotus rot. Significance of Impact of the Study The soil-borne fungus F. oxysporum causes lotus rot and severe yield loss, and currently available control methods are very limited. Here we identify a new promising biocontrol agent against lotus rot caused by F. oxysporum.