Molecular tags are becoming increasingly popular and useful for the study of biological macromolecules like proteins. Thus tags have been used to investigate structural and functional properties of proteins including their cellular/tissue distributions, localizations, imaging, interacting partners, trafficking routes, isolations, purifications and characterizations. Today, in-depth biochemical and functional research of proteins are possible due to the availability of specific molecular tags and their antibodies or ligands. As a result, chemical modifications of proteins with appropriate tags became an integral part of protein research. In most cases, these tags are attached via carboxyl (C) or amino (N-) terminal end of the protein. Alternatively, reactive side chain functional groups like SH, OH, NH2 or COOH groups of specific amino acid residues within the protein chain, can also be employed as connecting points for labeling agents. Fluorescent, radioactive or photo-labile tags in particular have been extensively used to study protein biosynthesis, localization, pathway analysis as well as its transient and ultimate final residence in real time manner in both cellular and animal systems. Attention has now been devoted to the development of tags that are selective to specific class of proteins such as phospho-, lipo- or glycoproteins in physiological systems. Moreover, proteins of all categories and residence types such as secreted soluble, membrane bound, cell surface, nuclear and mitochondrial proteins have been labeled with tags for various study purposes. This review provides a summarized report on the latest development in this field while presenting an up to date information on tags that are widely in use for today’s protein research.