The crystallization of calcium oxalates (weddellite and whewellite) by interaction of natural and synthetic apatites and fossilized tooth tissue with fungus Aspergillus niger, one of most active acid producers, was studied in vitro. The morphology and the sequence of formation of growing oxalate hydrate crystals were revealed. It was shown that morphogenetic patterns of calcium oxalate crystallization on apatite substrates under the action of Aspergillus niger micromycete are determined by the chemical properties of the crystallization medium, which depends on the solubility of the underlying substrate and on its chemical composition and structural features (dispersity and porosity). The main difference between oxalate crystallization under the influence of Aspergillus niger micromycete on the surface of apatite substrates and on the surface of calcite marble is the predominance of whewellite over weddellite on all stages of growth.