Organic crystals are of primary importance in pharmaceuticals, functional materials, and biological systems. Nevertheless, the understanding of organic crystallization mechanism is still limited. Understanding the transformation from “Non-classical” Prenucleation phases into crystals is a key challenge. In this study a Perylene Diimide (PDI) crystallization, within aqueous solution, is studied by optical spectroscopy and cryogenic electron microscopy, in order to address this challenge. Direct imaging of evolving prenucleation phase reveals a fascinating complexity of a nonclassical crystallization path, providing new insights into organic crystallization mechanism.