In this work we show a new experimental methodology to obtain ZnSe nanocrystals in aqueous solution aiming their application as biophotonic probes. The nanocrystals were obtained using a simple procedure based on the arrested precipitation of ZnSe in aqueous solution in the presence of a thiol-alkyl stabilizing agent, in air and at room temperature. Using post-preparative experimental procedures on the colloidal particles, blue and green emissions were observed. The structural characterization (powder X-ray diffraction and electronic transmission microscopy) shows that the particles were obtained in the quantum confinement regime (d=2–4nm) and possess a zinc-blend crystalline structure. The optical properties of the suspensions were determined by electronic absorption, excitation and emission spectroscopies and are discussed in terms of their size and chemical compositions.