To better understand the formation mechanism of carbonate minerals by microbes, culture experiments with a duration of 70days were performed under the mediation of strain GW-M isolated from soil using modified Lagoa Vermelha (LV, a hypersaline coastal Lagoon, Rio de Janeiro, Brazil) medium with 6:1 Mg/Ca molar ratio. The results demonstrated that strain GW-M can mediate the formations of both high-Mg calcite and aragonite and that dumbbell-, cauliflower-, rhombohedra-shaped, and irregular minerals coexist in the modified LV medium. The amount of rhombohedra-shaped crystals increased significantly with culture time. A proposed mechanism for these formations is the following. Heterogeneous nucleation on the surface of the extracellular polymeric substances (EPS) always occurred, and carbonates with irregular shape existed in experimental products at any stages. The morphologies evolved from rod to dumbbell and finally to cauliflower. At the initial stage (till day 20), hydrogen ions and EPS secreted by the bacteria only influenced the microenvironment around the cells, and carbonates were precipitated on the surface of bacterial cells. At the middle and late stages (on days 45 and 70), microbes and their secretions influenced the whole medium. Under these conditions, rhombohedra-shaped crystals were formed when homogeneous nucleation occurred. In addition, the results of energy-dispersive spectrometry (EDS) showed that Mg contents in the synthesized carbonate minerals with rhombohedra-shaped were significantly lower than those of carbonates with other shapes, though relationship between morphology and species of mineral cannot be obtained by this phenomenon alone. These results shed further light on the mechanism of carbonate precipitation in the presence of microbes.