The origin of crystalline complex superstructures of biomaterials and the unique self-assembly mechanisms of their formations have attracted a great deal of attention recently. In this paper the crystallization of cystine hierarchical structures by a crystallization procedure that mimics the slow oxidation chemistry of l-cysteine to l-cystine is studied. The crystalline superstructures of cystine are identified by X-ray diffraction (XRD), micro Raman spectroscopy, and scanning electron microscopy (SEM). It is found that the formation of unique spherical or hexagonal shaped cystine hierarchical structures depends on the initial concentration of l-cysteine. A possible mechanism based on the self-assembly process of cystine crystals is proposed. Overall our study suggests that it is possible to control morphogenesis and the formation of cystine crystalline superstructures by a simple chemical method that mimics biomineralization.