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In order to study the effect of irrigation levels and plant growth promoting rhizobacteria on yield, some physiological and biochemical indices of rapeseed, a factorial experiment was conducted based on randomized complete block design with three replications in Agricultural Research Station of Ardabil, Ardabil, Iran in 2016. The factors included in the experiment were irrigation in three levels (irrigation withholding at 50% of flowering and pod formation stages, irrigation withholding at 50% of grain formation stage, full irrigation or control) and application of bio-fertilizers in four levels (no inoculation, inoculations with Nitrobacter, Psedomonas and Azospirillum). Results showed that water limitation decreased yield, quantum yield, stomatal conductance, chlorophyll index, linoleic acid, eicosenoic acid and palmitoleic acid, but increased erucic acid, arashidic acid and proline contents. Mean comparisons showed that the highest grain yield (1.62 ton ha-1), quantum yield (0.523), stomatal conductance (14.7 mmol m-2 s-1), chlorophyll content (32.9), linoleic acid (10.45%) and eicosenoic acid contents (1.34%) were obtained in inoculation with Azosprillum and full irrigation. The highest contents of erucic acid (2.89%) and arashidic acid (0.94%) were observed at no inoculation and irrigation withholding in grain formation stage. The maximum of proline content (1.52 μg g-1 FW) was obtained in inoculation with Azosprillum and irrigation withholding at flowering and pod formation stage. It seems that application of plant growth promoting rhizobacteria leads to improving of some physiological traits such as quantum yield, chlorophyll content, stomatal conductance and proline content and can be recommended for profitable canola production under water limitation conditions. [ABSTRACT FROM AUTHOR]