The influence of the primary structures of plant (Canavalia ensiformis) and bacterial (Bacillus pasteurii) ureases on the precipitation of calcium carbonate polymorphs in solutions of calcium salts and urea at room temperature was investigated. Despite a similar catalytic function in the decomposition of urea, these ureases exerted different influences on the crystal phase formation and on the development of unusual morphologies of calcium carbonate polymorphs. Spherical and uniform vaterite particles were precipitated rather than calcite in the presence of Bacillus urease, while the presence of Canavalia urease resulted in the precipitation of calcite only. Vaterite particles were shown to be built up of nanosized crystallites, proving the importance of nanoscale aggregation processes on the formation of colloidal carbonates. Reduction of the concentration of Bacillus urease in the reacting solution results in the formation of calcite crystals with a more complex surface morphology than the ones obtained by Canavalia urease. These differences may be explained by dissimilarities in the amino acid sequences of the two examined ureases and their different roles in nucleation and physicochemical interactions with the surface of the growing crystals, during the precipitation processes. This study exemplifies the diversity of proteins produced by different organisms for the same function, and the drastic effects of subtle differences in their primary structures on crystal phase formation and growth morphology of calcium carbonate precipitates, which occur as inorganic components in a large number of biogenic structures.