Introduction: Alpha-amylase is an important commercialized enzyme among the starch-hydrolyzing ones. The bacterial amylase is widely utilized in various sectors of industry due to its advantages to amylases derived from plant or animal sources. Also the use of agricultural products and their residues as inexpensive fermentation substrates has high impact on minimizing the cost of α-amylase production. The principle aim of this study is to optimize α-amylase production by Bacillus amyloliquefaciens using low cost agricultural resources with Response Surfaces Methodology (RSM). Materials and methods: The Effect of different amounts of the carbon source (extract of pea) and nitrogen source (cotton seed cake) on production of α-amylase by B. amyloliquefaciens using statistical methods of RSM was studied. Carbon and nitrogen sources were considered in 5 levels during the submerged fermentation and used central composite rotatable design with 10 experiments. Results: The best conditions for maximum production of α-amylase by B. amyloliquefaciens were pea extract of 75g/L and cotton seed cake of 33.3 g/L, so that in these conditions the enzyme production rate was 69.74 Uml-1. During optimization by RSM, it became clear that the level of the used nitrogen source (cotton seed cake) is more effective in producing bacterial α-amylase in submerged fermentation compared to the used carbon source (extract of pea). Discussion and conclusion: This study showed the importance of the relationship between nitrogen and carbon sources on production of α-amylase. The results showed that the RSM applied for optimizing parameters of submerged fermentation condition aimed at producing maximum quantities of α-amylase by B. amyloliquefaciens acts with high efficiency.