The goal of this study was to characterize pigments used in the murals of two Byzantine churches, from Kastoria, northern Greece. The identification of the iconographer was also investigated by comparing the pigments applied in the wall paintings of the churches. Pigment microsamples of various colors were collected and analyzed by environmental scanning electron microscopy coupled with an energy dispersive system to characterize the elemental composition. Raman spectroscopy was employed to collect molecular spectra for characterization of mineralogical phases. Hematite, cinnabar, and minium were identified in red surfaces. Brown and yellow colors were assigned to mixtures of iron oxides, iron hydroxides, and calcite. Mixtures of iron, lead, and mercury compounds were used to produce different hues in the murals. Black tones were prepared primarily using charcoal and bone black. Grey colors were produced by a mixture of black carbon with calcite; blue hues, by a mixture of iron oxides, calcite, and black carbon. The minerals used were similar for both churches. However, the green color was prepared either by green earth or mixtures of iron oxides and calcite. A modern pigment, lithopone, was also determined, demonstrating restoration or overpainting and thus complicating possible correlations. Based on these preliminary results, the wall paintings could not be ascribed to a specific iconographer.