To the best of our knowledge, there has been no investigation of non-classical crystallization on hydrophobic substrates occurring in natural systems. The work presented here investigates the early growth process of nacreous aragonite crystals. We found that, (1) the contact angle of organic membranes >90°, proving that the aragonite crystals grow on the hydrophobic substrate. (2) The periphery of the aragonite crystals is decorated with nanoparticles, which grow epitaxially on the earlier aragonite crystals. (3) Some nanoparticles exhibit a surprising overhanging attachment pattern, that is, a particle sticks at a position higher than the height of the substrate surface at that point, such that the space below the particle is not filled. The hydrophobic substrate has an effect on the non-classical crystallization of nacreous aragonite crystals.