The concentration of anthocyanins in fruits of “Assaria” pomegranate, a sweet Portuguese cultivar typically grown in Algarve (south Portugal), was monitored during storage under different conditions. The fruits were exposed to cold storage (5C) after the following treatments: spraying with wax; spraying with 1.5% CaCl2; spraying with wax and 1.5% CaCl2; covering boxes with 25 μc thickness low-density polyethylene film. Untreated fruits were used as a control. The anthocyanin levels were quantified by either comparison with an external standard of cyanidin 3-rutinoside (based on the peak area) or individual calculation from the peak areas based on standard curves of each anthocyanin type. The storage time as well as the fruit treatment prior to storage influenced total anthocyanin content. The highest levels were observed at the end of the first month of storage, except for the fruits treated with CaCl2, where the maximal values were achieved at the end of the second month. The anthocyanin quantification method influenced the final result. When total anthocyanin was calculated as a sum of individual pigments quantified based on standard curves of each anthocyanin type, lower values were obtained.