Georgia’s blueberry industry consists of southern highbush (SHB, Vaccinium corymbosum L. and V. darrowii Camp complex) and rabbiteye (RE, V. virgatum Aiton). There exists a subjective bias that SHB has higher fruit quality than RE. Their quality is also compared to northern highbush (NHB, Vaccinium corymbosum L.), which is perceived as superior. However, limited information supports this preconceived perception. The objective of this study was to examine the physicochemical postharvest keeping quality of major SHB, RE, and NHB cultivars and examine their differential gene expression relating to their keeping quality. During postharvest storage, the highest texture stability was by SHB, visual appearance by SHB and NHB, and berry weight by RE. Chemical quality traits were generally stable. Gene expression analyses revealed three genes involved in cell wall degradation differed over storage and types. Overall, this may help the industry in selecting and developing new cultivars with superior postharvest keeping quality.