We developed a method to detect and identify proteins on a probe of the atomic force microscope (AFM) with a high sensitivity. Due to a low background noise of the total internal reflection fluorescence microscope employed as a detecting system, we were able to achieve a high enough sensitivity to detect zeptomole orders of protein molecules immobilized on the tip. Several different methods to immobilize protein molecules to AFM-probes were tested, meant for a wide range of applications of this method. Furthermore, we demonstrated that different proteins were clearly distinguished by immunofluorescence microscopy on the probe using their specific antibodies.