Objective To isolate and identify highly effective strains capable of removing chemical oxygen demand (COD) and ammonia nitrogen from antibacterial wastewater.Methods Metagenomic sequencing technology is employed to deeply explore the microbial resources in wastewater isolated by freshly-extracted Zanthoxylum oil. The strains with the ability to efficiently remove COD and ammonia nitrogen are accurately analyzed. The strains with pollution-reducing potential are screened from wastewater enriched through natural outdoor cultivation for one month.Results Proteobacteria and Firmicutes are the predominant phyla in the wastewater isolated by freshly-extracted Zanthoxylum oil, while Enterobacter and Acetobacter are the dominant genera. Three strains with significant COD and ammonia nitrogen removal capabilities are selected and identified as Bacillus stercoris strain X4, Pseudomonas putida X21, and Pseudomonas taiwanensis X22. In actual wastewater treatment, the COD removal rate of these three strains after 8 days is 55.47%, 50.76%, and 52.32%, respectively, while the ammonia nitrogen removal rate after 36 hours is 55.93%, 54.19%, and 40.79%, respectively.Conclusion The strains identified through indigenous enrichment in Zanthoxylum oil wastewater are more effective in reducing pollution than those from other sources.