The structural forms of cyanidin and cyanidin 3-O-β-glucopyranoside (Cy3Glc) were investigated in the pH range from 0.4 to 13.5 for cyanidin and 0.4 to 13.2 for Cy3Glc. The 3-glucosidic substitution in cyanidin 3-O-β-glucopyranoside at pH values lower than 4.0 was manifested in a large hyperchromic effect, while at pH values higher than 4.0 had the opposite effect and resulted in high hypochromic effect. Multivariate data analysis showed that the structural forms of cyanidin and Cy3Glc have numerous bends, which mutually overlap and influence the shape, position, and intensity of their spectrophotometric measurements. For cyanidin seven structural forms were identified, while for Cy3Glc six structural forms were identified, and one was not. To determine the stability of cyanidin and Cy3Glc at different pHs, HPLC–DAD–ESI/MS analysis was performed. The stability was tested in buffers at four pH values between 2 and 9. Degradation products formed from cyanidin and Cy3Glc at different time in the different buffer solutions were tracked and some of them were identified. Cyanidin stability was decreased in the following order pH 7.0, pH 4.0, pH 2.0, pH 9.0. Stability of Cy3Glc was increasing with decreasing the pH. Cy3Glc was the most stable at pH 2.0, and the least stable at pH 9.0.