Herein, we demonstrate a simple hydrothermal route to synthesizing ZnSe/ZnO type II heterostructure using L-cysteine as a capping agent. The use of nanomaterials in bioimaging and photocatalysis towards the degradation of Azophloxine dye is of potential interest. The synthesized ZnSe/ZnO nanomaterials were characterized by UV-Vis absorption spectroscopy, fluorescence spectroscopy, IR spectroscopy, scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. It exhibits a strong sharp emission at 465 nm in fluorescence spectroscopy. The synthesized nanomaterials were used as an excellent fluorescence probe for imaging live-cell bacteria such as E. coli and S. aureus compared with the commercial staining dye PI (propidium iodide). The synthesized ZnSe/ZnO possess more photo-stability and showed excellent photocatalytic activity for the degradation of azophloxine dye under sunlight.