In this study, microwave assisted NaOH pretreatment of wheat straw was thoroughly investigated using central composite design (CCD) under varying operating variables. i.e. pretreatment time, temperature and NaOH concentration. The crystallinity, crystalline length, surface microstructural change, functional group change and compositional analysis of both optimally pretreated and untreated wheat straw samples were studied. Microbial hydrolysis by Bacillus sp. BMP01 and bioethanol production was also tested for the optimally pretreated wheat straw sample. The pretreatment condition at 160 degrees C, 1.5% NaOH concentration and 15 min preserved high cellulose and removed high amount of lignin. At this point 38.34% of hemicellulose and 74.15% of cellulose were preserved in the solid residue and 69.49% of lignin was solubilized. An overall increase in crystallinity (from 0.3780 to 0.5610) and crystalline length (from 2.51 to 4.83 mu) were observed after the pretreatment process. Mathematical models were developed to predict the lignin removal, cellulose preserved and hemicellulose solubilization during microwave assisted NaOH pretreatment process. 718 mg/g of reducing sugar was released after hydrolysis pretreated wheat straw by Bacillus sp. BMP01. Ethanol yield of 68.2% was obtained after 96 h of fermentation. It was found that the combination of microwave assisted NaOH pretreatment at optimal condition coupled with microbial hydrolysis and C5 and C6 fermenting microbes enhanced reducing sugar and ethanol yields.