An analytical scheme for the fractionation and the determination of Ca and Mg in different bee honeys is presented. Using tandem column solid phase extraction based on a nonionic macro-reticular adsorbing resin Amberlite XAD-16 and a gel-type strong cation exchange resin Dowex 50Wx8-200, three different groups of the Ca and Mg species were separated, including the hydrophobic, the cationic, and the residual species fractions. The concentrations of Ca and Mg were measured by means of flame atomic absorption spectrometry without any special chemical preparation of the analyzed samples. When regarding the total concentrations of Ca and Mg in the analyzed ripened floral and honeydew honeys, it was assessed that the most abundant group of the metal species was the cationic fraction, contributing for some honeys up to 96.3 and 97.0% of Ca and Mg, respectively. A relatively significant contribution of the hydrophobic fraction was also found, i.e., up to 20.1% for Ca and 23.0% for Mg.