Metals and mineral flotation collector's toxicity to the soil living system greatly compromise the sustainability of mining and ore processing. Their effects on the soil microbial community, the most active soil component, remain less understood and addressed particularly with regards to xanthates and their combination with metals. This study analyzed the interactive effects of Ni and xanthates, potassium ethyl xanthate and sodium isopropyl xanthate, on the soil bacterial community through an efficient molecular biology-based technique, the Miseq (Illumina). Both soil microbial community diversity and structure were more affected by xanthates than by Ni. The five most dominant phyla, representing 96.31% of the whole bacterial community, comprised Proteobacteria (54.16%), Firmicutes (17.51%), Actinobacteria (15.59%), Acidobacteria (4.87%), and Chloroflexi (4.16%). Different soil treatments exhibited greater difference in the species abundance/dominance than in the species numbers. Proteobacteria was the most dominant in the presence of xanthates, individually or in mixtures with nickel, while Firmicutes exhibited its highest proportion in the Ni/xanthate-treated samples. The most abundant and proportionally different bacterial species between different treatments were presented. The most abundant bacterial strains identified should be explored more for their potential application in biomining and for the prediction and biologically-based treatment and remediation of Ni and xanthate-contaminated systems.