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Effects of Rhizobium inoculation on plant height (PH), leaf area (LA), leaf net photosynthesis (Pn), leaf transpiration rate (Tr) and water use efficiency (WUE) of stony desertification-grown white clover (Trifolium) by Rhizobium sp. SWFU27, SWFU29 were studied during Spring 2011. Seeds were soaked for 30min in strain SWFU27, SWFU29 cell suspensions respectively, growing individually in autoclaved stony desertification soil under nursery conditions at ambient temperatures. Datum were collected from 90-day-old plants on a sunny day. Rhizobium inoculation by SWFU27 significantly increased PH and LA by 50% and 91.58% separately, and SWFU29 by 129.17% and 158.95. Pn, Tr, WUE for three sets of plants all in turn: SWFU29 > SWFU27 > CK, suggesting that maximum growth of stony desertification-grown plant requires the Rhizobium inoculation to promote the growth, between the two inoculation systems, SWFU29 had a high photosynthesis efficiency, transpiration potential and water use efficiency than SWFU27 and SWFU29 is much light-tolerance species than SWFU27, thereto signify the phenomena that white clover inoculated by Rhizobium sp. SWFU29 is growing better and to be a pioneer dominant in Karst stony desertification area.