Endophytic bacteria Ochrobactrum intermedium AcRz3 obtained from ethnomedicinal plant Acorus calamus rhizome exhibited growth inhibition against five fungal pathogens, showing highest and lowest inhibition percentage of 73 and 65 against Rhizoctonia solani and Helminthosporium oryzae. Isolate showed positive results for chitinase, protease and lipase but negative for β, 1–4 glucanase production. The strain could produce 29.61 μg/ml of IAA and 72% of siderophore. It could solubilize significant amount of P up to 102 μg/ml. The strain showed negative results for ACC deaminase production. The strain enhanced seed germination and significantly promoted the growth of black rice seedlings. The strain significantly promoted the growth and grain yield production of black rice plants under net house conditions. Similar results were also observed under R. solani challenged conditions. The isolate significantly protected the lesion caused by R. solani. Endophytic strain AcRz3 associated with medicinal plant had great potential to be exploited for application as biocontrol and biofertilizing agents for rice production.