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The precipitation of carbonate minerals induced by halophilic bacteria has aroused wide concern. The study aimed to investigate the characterization and process of biomineralization in high salt systems by halophilic Chromohalobacter israelensis LD532 (GenBank: KX766026) bacteria, isolated from the Yinjiashan Saltern in China. Carbonate minerals were induced in magnesium sulfate and magnesium chloride medium, respectively. The mineral phase, morphology, and elemental composition of minerals were analyzed using X-ray p owder diffraction, scanning electron microscopy, and energy dispersive X-ray detection. Cells and ultrathin slices were studied using high resolution transmission electron microscopy, selected area electron diffraction, and energy dispersive X-ray detection. The carbonic anhydrase and ammonia released from LD532 bacteria increased pH of the medium and promoted the carbonate precipitation. Magnesium calcite and aragonite were induced by LD532 bacteria in magnesium chloride medium at an Mg/Ca molar ratio of 2, while Magnesium calcite and monohydrocalcite were precipitated in magnesium sulfate medium at the same Mg/Ca ratio, only monohydrocalcite were formed in both control groups. The morphologies and compositions of minerals in MgSO4 and MgCl2 solutions displayed significant differences, indicating different Mg2+ could affect physiological and biochemical activities of LD532 bacteria and thus affect the mineral deposition. Further study showed the nucleation sites were located on extracellular polymeric substances and intracellular vesicles of LD532 bacteria. This study is beneficial to the mechanism of carbonate biomineralization in natural salt environments.