This research compared expression patterns of aquaporin (AQP) genes in two apple cultivars that exhibit contrasting ripening behavior. Commercially-mature apple fruits of cultivars ‘Golden Delicious’ and ‘Red Fuji’ were chosen as materials. The results showed that compared with ‘Red Fuji’, ‘Golden Delicious’ generally had higher rate of respiration, ethylene production, weight loss, dry matter concentration (DMC), titratable acidity (TA), total soluble solids (TSS) and soluble sugar contents during ripening. At 35 d, cells in ‘Golden Delicious’ were loosely arranged with larger intercellular space, while in ‘Red Fuji’, cells were still densely packed. A total of 20 AQPs were detected in both cultivars. Expression of these identified genes was in a tissue- and cultivar-specific manner during ripening. Generally, expression of MdAQPs was differentially induced at climacteric stage in peel and flesh tissues of ‘Golden Delicious’. In contrast, expression of most MdAQPs was differentially up-regulated at preclimacteric stage in peel and flesh tissues of ‘Red Fuji’. These results will be useful for further study the relationships between MdAQPs and storability of different apple cultivars.