Rhizobacteri indigenous Merapi Isolates have been characterization, and MA, MB, and MD isolate could withstand osmotic stress up to >2.75 M NaCl. MD isolate was stronger in dissolving Phospate than MA and MB isolate, but MA and MB isolate had much stronger Nitrification capability and could perform ammonification than MD isolate. Rhizobacteri indigenous Merapi could grow in rice plant rhizosphere in drought stress, despite the need to adapt until the 3rd week and highest mix of MA-MB-MD isolate (76.68x109 cfu/ml), although it depends on the moisture degree. Rice plant in water stress (KL 40%) clearly better influence against all rice plant growth parameter. There is reciprocal influence between the mix of MA-MB-MD isolate treatment and watering frequency which shows in rice plant growth indicator (root and crown), but still no effect on rice product.. The effect of once per day watering without inoculation was the same with MB-MD inoculation isolate with once per three days watering, even with once per 6 days watering with MA-MB-MD mix isolate inoculation. It is expected that the formulation of Rhizobacteri Indigenous Merapi could be utilized as bio fertilizer to increase rice plant tolerance against the stress of drought.