A novel microbial consortium (BM-S-1) enriched from the natural soils was successfully implemented to treat the tannery wastewater from leather manufacturing industries in Korea in a pilot scale and full scale system in China without chemical pretreatment. The full scale tannery system was built after the pilot system has been proven effective. Chemical oxygen demand (COD), total nitrogen (TN), total phosphorus (TP), chromium (Cr) and mixed liquor suspended solids (MLSS) were measured to monitor treated water quality and treatment efficiency. Microbial population dynamics were analyzed using pyrosequencing and denitrifying bacteria was quantified using real-time PCR (RT-PCR) of the nitrous oxide reductase gene (nosZ) in both systems. Removal efficiencies for COD, T-N and T-P were more than 91%, 79%, and 90%, respectively for the pilot system while the removal efficiencies of COD, TN, TP, and Cr were 98.3%, 98.6%, 93.6%, and 88.5% in the full scale system. In the pilot system, the dominant phyla in buffering tank (B), primary aeration (PA), secondary aeration (SA) and sludge digestion tank (SD), were Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes and Deionococcus-Thermus while the full scale system contained Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi and Deinococcus-Thermus. Cluster analysis based on unifrac distance of the species in the different stages showed that the microbial communities in PA is similar to SA while B is closer to SD in the pilot system, B is closely related to PA and SA to SD in the full scale. The qPCR of nosZ genes showed the highest abundance of denitrifiers in B increasing 734 folds compared to the influent (I) in the pilot system while the abundance of denitrifiers increased approximately 195 times in B, as compared to the influent of wastewater, and after the BM-S-1 consortium augmentation in the full scale treatment system. The pyrosequencing analysis of the pilot system showed AB430337_f_uc_s, Methyloversatilis_uc, AB430336_s, were the most abundant species while Brachymonas denitrificans was the most abundant in full scale especially in B (6-37.5%). Other polymeric substance degraders (Clostridia), sulfate reducers (Desulfuromonas palmitatis), and sulfur oxidizers (uncultured Thiobacillus) were dominant in the sludge digestion (SD) tank. Whole-metagenome sequencing analysis using Illumina MiSeq Sequencer was done to determine microbial community structures and functional genes associated with treatment of tannery wastewater in the full scale treatment system. The metagenome sequencing data demonstrated that four phyla were Proteobacteria, Bacteriodetes, Firmicutes and Actinobacteria were dominant in the treatment process. The genes involved in metabolisms of carbohydrates, protein and amino acids were more than 80% compared to the genes associated with metabolisms of lipids and fatty acid, nitrogen, sulfur and phosphorus that were less than 70% in B and PA. For nitrogen metabolism, genes associated with ammonia, nitrate and nitrite assimilation were more abundant than the genes responsible for denitrification and dissimilatory nitrite reductase. The dominant genera involved in nitrogen metabolism were Burkholderia, Polaromonas, Albidiferax, Acidovorax, Geobacter, Dechloromonas, Pseudomonas, and Rhodopseudomonas. Glutamate synthase, glutamate dehydrogenase, nitrous oxide reductase and nitrate reductase were distinctively observed depending on the kinds of these genera. Glutamate synthase (GS) and glutamate dehydrogenase (GDH) were abundant in Burkholderia, Delfia, Bordetella Albidiferax, Acidovorax, Cupriavidu genes such s, Thiobacillus, Methylibium, Azoarcus, Dechloromonas, and Aromatoleum while as nitric oxide reductase and nitrate reductase (NAR) showed high abundance in Geobacter, Burkholderia, Acidovorax, Cupriavidus, Thiobacillus, and Chromobacterium in the different stages of the treatment process. Most of the metabolic processes were relatively more active in PA and B which corroborated with the chemical data (COD, T-N and T-P, etc.) obtained from all the stages during the treatment process. These results provide a detailed understanding into the structures and functions of the microbial communities in the eco-friendly tannery wastewater treatment. Furthermore, these data would provide useful information for designing the full scale treatment system.