In this work, we report the synthesis of ZnS nanostructures by a simple and eco-friendly method that makes possible producing nanoflakes at room temperature. Scanning electron microscopy and transmission electron microscopy methods (mainly bright-field, high resolution and high angle annular dark-field) were used to identify and study the obtained nanostructures. The structure of these nanoflakes consists of nanosized crystalline particles around 1.5 to 3 nm. Domains with different contrast of nanometer-size diameters are formed in the self-assembled nanoflakes as a result of a noncompact arrangement of nanocrystallites during agglomeration and differences in the presence of the organic passivation agent. Agglomeration can be attributed to the amount of crystallites generated at the beginning of the reaction or to an anisotropic interaction between phosphate ions and the surfaces of ZnS clusters, and consequently a bottom-up synthesis is considered, which opens a simple route for the production of nanomaterials with the inclusion of extra elements by a simple way.