A new nanohybrid material with a potential impact on energy transfer processes in biomolecules was developed by coupling colloidal fluorescent semiconductor CdSe/ZnS quantum dots (QDs) with a photochromic membrane protein, the bacteriorhodopsin (bR). The interactions between the nanocrystals and the proteins were studied by fluorescence spectroscopy and atomic force microscopy (AFM) measurements. A quenching in the photoluminescence (PL) of QDs emitting in the range of the bR absorption suggests a fluorescence resonance energy transfer effect from QDs (donors) to bR (acceptor). As the quenching evolution is different with the surface charges of the QDs, it suggests that the QDs interact with bR through electrostatic interactions. The AFM images of bR coupled with QDs capped with positive or negative surface groups confirm that the electrostatic interactions between QDs and bR play a dominant role in the way they are coupling together. The observed interactions between QDs and bR can provide the basis for the development of novel functional materials with unique photonic properties and having applications in the all-optical switching, photovoltaics and data storage.