To evaluate the influences of cyanobacterial extracellular polymeric substances (EPS) on CaCO3 precipitation, calcification experiments were conducted for 48 h (initial values of calcite saturation state and equilibrium CO2 partial pressure were ∼5-fold and ∼600 μatm, respectively) using cultures of four filamentous strains (Leptolyngbya sp. (NIES-2104), Scytonema sp. (NIES-2130), Phormidium ambiguum (NIES-2119), and Spirulina subsalsa (NIES-598)). All cultures induced CaCO3 precipitation mainly by photosynthesis to form mono-/poly crystalline calcite and amorphous calcium carbonate (ACC) around them. These features suggested a CaCO3 nucleation process via an ACC precursor phase on negatively charged substances generated by cyanobacteria (i.e., cell walls, EPS, and oxygen bubbles). The characteristics of the precipitated CaCO3 were strongly influenced by the surface properties of the cyanobacteria. For Leptolyngbya, which lacks EPS, a small number of CaCO3 was nucleated onto the smooth surface of negatively charged cell walls and entire cells were incorporated into a large single crystal of calcite. For Scytonema and Phormidium, which possess EPS sheaths, a relatively large number of CaCO3 was nucleated onto the rough surface of negatively charged sheaths, and their sheaths were encrusted and partially impregnated by calcite crystals. For Spirulina, which possesses a loose EPS matrix, CaCO3 nucleation was scarce and restricted to the surface of negatively charged oxygen bubbles stabilized by the EPS matrix to form hollow calcite crystals. These results suggest that chemical properties (i.e., abundance of dissociated acidic groups) primarily controlled the presence/absence of CaCO3 nucleation around cyanobacteria, while a physical property (i.e., submicron-scale structure of negatively charged substances) primarily controlled the numbers of crystal nuclei provided and stabilized ACC precursors as well as the calcification styles (sheath encrustation or impregnation).