A novel biocompatible chitosan passivated manganese doped zinc sulfide (Mn doped ZnS) nanophosphor has been synthesized through a simple aqueous precipitation reaction. Upon excitation with ultraviolet light, the quantum dots (QDs) emit an orange luminescence peaking at 590 nm, which is visible to the naked eye. These chitosan coated Mn doped ZnS QDs can have potential applications in bio-labeling, particularly in fluorescence-based imaging. One of the envisioned applications of these QDs is in improving the conventional, organic dye-reliant Fluorescence in situ Hybridization (FISH) technique, a widely used method for microbial detection. Here we demonstrate that the chitosan-capped Mn doped ZnS QDs are suitable for this purpose.