Mediterranean Sea Lithophaga bivalve associated bacteria and their capability in calcium carbonate polymorphs formation have been investigated in the present study. Isolated bacteria were a single strain of Gram-negative, rod-shaped, and flagellated motile cells. Phylogenetic analysis based on 16S rDNA sequences consigned the isolated bacterium to Alcaligenes aquatilis species as a distinct strain assigned as Alcaligenes aquatilis strain MAG 1. Phenotypic and biochemical characteristics of the strain recorded no acids produced from different carbohydrates under aerobic conditions except for D-mannose, amygdalin, glucose, L-rhamnose, L- arabinose and D- melibiose. Isolates showed negative results for nitrate reduction, urea degradation, sulphate reduction (H₂S production) and tryptophan deaminase (TDA). Alcaligenes aquatilis strain MAG 1 precipitated in nutrient-free medium different polymorphs of anhydrous CaCO₃, initially, as a mixture of aragonite and calcite, and well-organized rhombohedral calcite crystals dominated by the fourth day. Conclusively, calcium carbonate biomineralization away from any added nutrients by this new strain magnifies its role as nucleation sites and retracts the effect of bacterial metabolic pathways. Besides, various CaCO₃ crystal polymorphs formed by the isolated strain advocate a potential complementary role in Lithophaga shell assembly.