Blueberry surface color is determined in large part by anthocyanin pigments and is one of the most important quality traits influencing consumer preference. Postharvest changes in fruit surface color and phenolic compounds, including anthocyanins, have been reported in blueberries; however, the relationships between these changes had not yet been investigated. A total of 25 anthocyanins and 14 flavonols were quantified across 20 blueberry genotypes at harvest and during four weeks of postharvest storage in 2019 and 2020. Total anthocyanin concentration ranged from 585.4 to 2556.4 mg kg‐1 across genotypes and was higher than total flavonol concentration that ranged from 129.3 to 331.0 mg kg‐1. Malvidin glycosides were the major anthocyanins in all genotypes; however, distinct anthocyanin profiles were observed among genotypes based on differences in the type of glycosylation. Quercetin 3-O-galactoside was the most abundant flavonol in all genotypes. Changes in total anthocyanin and total flavonol concentrations showed various trends during storage, depending on the genotype and the season. In contrast, anthocyanin and flavonol profiles for each genotype remained constant during storage and between seasons. Surface color parameters (lightness, chroma, and hue angle) showed weak correlations (r < 0.4) with anthocyanin concentrations measured at harvest and during postharvest storage. However, the color changes (Δ color) over four weeks of storage showed a strong correlation (r > 0.7) with changes in anthocyanin concentrations. This study provides novel understanding of the relationship between changes in anthocyanins and fruit surface color during postharvest storage in blueberries. •Anthocyanin profiles vary among blueberry genotypes by the type of glycosylation.•Season and postharvest storage time have limited effects on anthocyanin profiles.•Variations in anthocyanins at harvest do not determine variations in fruit color.•Postharvest changes in anthocyanin levels and fruit color do correlate.