Fluorescence is a phenomenon in which a fluorophore passes into an excitation state by absorbing a photon of the light of certain wavelength. While the fluorophore is in the excitation state, part of the energy is transferred to the adjacent molecules or lost due to molecular collisions. Ultimately, the molecule returns to its basic state, while emitting energy as a photon. There are three general groups of fluorescent molecules: biological fluorophors, quantum dots and organic dyes. The most common use of fluorescent molecules is in fluorescent labeling. Namely, fluorescent labeling entails the covalent binding of a fluorophore to another molecule, such as a nucleic acid or a protein. Generally, this can be accomplished by using a reactive derivative of a fluorophore which is capable of selectively bind to a functional group present in the molecule of interest. This paper discusses the fluorescence labeling of proteins using organic dyes. The functional group of a certain fluorescent dye is linked to the corresponding functional group in the protein, most often of which are primary amines, carboxyl groups, sulfhydryl groups and carbonyl groups. Furthermore, this work discusses the various functional groups which are most commonly used in protein labeling. Also, in this work are listed some of the examples of the most widely used fluorescent dyes, and the compound 5-(4-carboxyphenyl)-2,8-diethyl-1,3,7,9- tetramethyldipyrimomethene (BODIPY-COOH) (1) and its reactive derivative 5-(Nsuccinimidoxycarbonyl) phenyl)-1,3,7,9-tetramethyl-BODIPY (2) have been synthesized. The synthesized dye (2) is the most commonly used dye for conjugation with amino-containing structures, therefore it is of great importance in the context of bio-labeling.