Aims: In recent studies, xylanase is the valuable enzyme in paper industry, and the demand of this enzyme is increasing. The finding out of the new xylanases with good properties and applicable for paper industries from Indonesian biodiversity is still required. In this study, we isolated, cloned, and expressed the gene encoding alkalophilic xylanase gene from Indonesia indigenous Bacillus halodurans CM1 in Escherichia coli, and applied the recombinant xylanase in deinking process. Methodology and results: The open reading frame of the gene consist of 1191 bp, with nucleotide identity 99% with that of B. halodurans C-125 has been obtained by using PCR. The gene was submitted into GenBank with accession number KU759320. The gene was then subcloned and expressed in E.coli using pET 21d(+) vector, and we found that only extracellular that have significant activity. The gene product had optimum activity at 65 °C and pH 9. After purification using Ni-NTA, the single band was obtained, and the molecular mass was about 45 kDa based on SDS/PAGE analyses. The recombinant xylanase had been applied in deinking process of old news paper at laboratory scale of a paper industry. This recombinant xylanase application showed better brightness and whiteness, as well as higher brightness and whiteness gain of of product compared to the commercial one when using the same raw material. Conclusion, significance and impact of study The study is the first example of the cloning of industrially important enzyme (xylanase) from B. halodurans CM1 and showed potential application of the recombinant enzyme in deinking process of waste paper.