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The undigested phytic acid excreted in animal waste causes phosphorus pollution from agriculture. Addition of microbial phytases to animal feeds is a promising approach to overcoming challenges posed by phytic acid. In this study, influence of physicochemical parameters on growth and production of phytase from Bacillus amyloliquefaciens PFB-02 was investigated over 96 h cultivation period. Effects of some readily available and low cost agricultural wastes on phytase production from B. amyloliquefaciens PFB-02 were also investigated. Maximum growth with phytase yield of 5.3 U/ml was achieved in the basal medium at 48 h cultivation period, pH 5.0, 40 °C and 180 rpm. The optimized conditions were used to study phytase production from B. amyloliquefaciens PFB-02 grown on wheat bran, black-eyed bean skin and rice bran based media under submerged fermentation conditions. Remarkably, wheat bran supported highest enzyme yield of 17.0 U/ml with 317.5% increase over yield in basal media. Rice bran and black-eyed bean skin also supported phytase production from B. amyloliquefaciens PFB-02 with yield of 4.6 U/ml and 3.5 U/ml, respectively. The results suggest that agricultural wastes are effective low cost substrates for phytase production from B. amyloliquefaciens PFB-02 for potential application in animal feed formulation.