Based on analogy between quantum mechanics and the classical electrodynamics, we sorted dielectric microspheres with almost identical positions of their whispering gallery mode (WGM) resonances as photonic atoms. Such microspheres were assembled in a wide range of structures including linear chains and planar photonic molecules. We studied WGM hybridization effects in such structures using side coupling by tapered microfibers as well as finite difference time domain modeling. We demonstrated that the patterns of WGM spectral splitting are representative of the symmetry, number of constituting atoms and topology of the photonic molecules. Such splitting patterns can be viewed as “spectral signatures” of corresponding molecules. Excellent agreement was found between measured and calculated fiber-transmission spectra for different molecules.