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Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (<i>w</i>/<i>v</i>) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of <i>Lysinibacillus pakistanensis</i> LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of <i>Lysinibacillus</i>, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of <i>Lysinibacillus</i>, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of <i>Lysinibacillus</i> spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in <i>Lysinibacillus</i> spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of <i>L. pakistanensis</i> to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that <i>L. pakistanensis</i> LZH-9 was promising in treating hypersaline industrial wastewater.