Hydrogen sulfide (H2S) is highly corrosive to electric generators, which is the main problem of biogas utilization. The industrial scale of the biofilter system relies on the performance of sulfide-oxidizing bacteria (SOB) via the activity of sulfur oxidation (soxABXYZ) and flavocytochrome sulfide dehydrogenase (fccAB) enzymes to reduce to a concentration below 100 ppm before using in industrial machinery. The main purpose of this research is to investigate the SOB community in full-scale H2S removal and their gene expression (fccAB and soxABXYZ) associated with H2S elimination efficiency. In this study, SOB communities were obtained from 2 sampling sites of the full-scale biofilter of palm oil factory (PPG), comprising starting sludge (PPG1) and recirculating sludge (PPG2). The abundance of SOB strains was examined by next-generation sequencing analysis (NGS) based on the 16S rRNA gene. The changes in the expression of genes involved in sulfur oxidation, namely soxABXYZ, and fccAB, between the 2 sampling sites were evaluated by using a comparative genomic hybridization (CGH) microarray. The results indicate that the high abundance of SOB genera that could play a vital role in biofilters belonged mainly to Sulfurovum, Paracoccus, Acidihalobacter, Acidithiobacillus, Thioalkalispira, Thiofaba, Caldisericum, Bacillus, were rapidly increased in the biofilter tank. Interestingly, expressions of soxAXYZ gene cluster at PPG2 were increased in Paracoccus pantotrophus J40 and Paracoccus alkenifer DSM 11593 for 1.1188 and 1.0518-fold, respectively, while in Acidihalobacter prosperus F5, the expression of fccAB genes was up to 1.3704 fold in comparison with PPG1. Increasing both relative abundance and gene expressions at PPG2 were correlated with 95% H2S removal efficiency. Hence, stabilization of the SOB microbiome is vital to H2S removal in industrial-scale biogas applications.