Abstract: The formation mechanism of dolomite [CaMg(CO₃)₂] remains a longstanding enigma in earth sciences. Previous studies have identified certain microorganisms and clay minerals as catalysts in the crystallization of low-temperature protodolomite, a crucial precursor to ordered dolomite. However, the role of cyanobacteria and particularly their potential synergistic effects with clay minerals remain poorly understood. In this study, we investigated bioprecipitation of carbonate minerals using the halotolerant cyanobacterium Synechococcus elongatus FACHB-410 in the presence and absence of montmorillonite. Our results demonstrated that protodolomite occurred as the predominant solid product in the montmorillonite-amended biosystems as confirmed by X-ray diffraction and Raman spectroscopy, whereas monohydrocalcite and low-magnesian calcite were the primary products in the montmorillonite-free biosystems. Multiple microscopic techniques, including scanning electron microscopy, focused ion beam microscopy, and transmission electron microscopy, revealed that protodolomite nucleated as nanocrystals preferentially on montmorillonite surfaces. Density functional theory simulations further elucidated that surface electronegativity of montmorillonite played a key role in promoting protodolomite formation by strongly adsorbing Mg²⁺ ions through electrostatic interactions, thereby facilitating their dehydration and significantly lowering the nucleation energy barrier.