Aims: Termites thrive in terrestrial ecosystems and play an important role in the bio-recycling of lignocellulose. The objective of this study is to isolate and detect bacteria from the termite gut of Coptotermes formosanus and to screen their various enzyme activities by qualitative methods. In addition, this study was aimed to isolate lignin and furfural tolerant strains for various industrial bioprocesses. Methodology and Results: In this study, 50 worker termites of Coptotermes formosanus were collected from dead trees, from a forest in Taichung, Taiwan in June 2008 and the composition of the microbial flora from the termite guts was analyzed by DGGE analysis. The results proved that anaerobic and facultatively anaerobic bacteria consisting of Acinetobacter, Bacteroides thetaiotaomicron, Escherichia coli, and Caulobacter readily existed in the guts of termites. Although the majority of these gut symbionts have not yet been cultivated or identified, some related bacteria were isolated. Two isolates 1-8 and 2-2 of Genus Bacillus, exhibited endocellulase, protease, lipase, amylase, peroxidase and lignin peroxidase activity. Under aerobic conditions, the growth density of isolate 1-8 cultured in 1000 ppm lignin containing MSM medium was two-folds higher than cultured in MSM medium without lignin. Furthermore, the isolate 1-8 was tolerant to 20 mM furfural supplemented in the MSM medium. HPLC analysis confirmed Bacillus isolate 1-8 could degrade up to 15 mM furfural. Conclusion, significance and impact of study: Hind gut bacteria from C. formosanus were detected by culture independent DGGE method. Also, Bacillus isolates 1-8 and 2-2 obtained by culture dependent methods could withstand higher concentration of furfural and as well as lignin. These isolates may be co-cultured with ethanologenic bacteria and be used as an industrial biocatalyst for biofuel production.