At present study, a C-D fragment of bacteriorhodopsin (BR) in recombinant E. coli was expressed. BR mutant gene was synthesized by consideration of E. coli codon usage. The synthesized gene was cloned in pET21a+ expression plasmid at Nde J and Hind 111 restriction sites and expressed under T7 promoter successfully. The expressed protein was analyzed by SDS-PAGE. The effect of temperature (A), induction time (B) and the process time after induction (C), on the protein expression yield (the amount of product per unit dry cell mass) were screened using Yates table analysis. Three factors of A, Band C were significant and optimized by Taguchi method. The optimized condition was as: temperature 37oC, induction time at OD600=0.7 and the process time after induction 4 h. Also, the predicted protein production at optimized condition was 21.54% of total protein. Using the gained optimum condition, the effect of amino acid addition on expression level of recombinant C-D fragment of BR and bacterial growth in E. coli, using M9 culture medium was also investigated. Yates table analysis showed that Threonine, Leucine and Alanine are more effective and so were selected for addition to the culture medium in the fermentor, at two different levels. The results showed that amino acid addition caused increasing in the desired protein productivity, but had little effect on the bacterial growth.