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.