Cultivars of the same species exhibit a large degree of variation in fruit quality traits, which can be directly influenced by differences in gene expression due to allelic variations and interactions with the environment. For Malus × domestica Borkh. (apple), fruit quality traits, including color, texture, aroma, flavor profile, and shelf life, are of utmost economic importance. In order to identify genes potentially influencing these traits, a direct comparative transcriptome profiling approach, based on the differential display technique, was performed using “Golden Delicious” and “Honeycrisp” apple endocarp and peel tissues. A total of 45 differentially expressed sequence tags were identified between the two apple varieties. Reanalysis of a previously published fruit developmental microarray expression experiment revealed that only one of the 45 sequence tags was represented on the array. Differential expression of 31 sequence tags from the peel tissue was validated using quantitative reverse transcription PCR, confirming the robustness of the differential display approach to quickly identify differentially expressed sequence tags. Among these were genes annotated to be involved in ripening, phytohormone signaling, transcription factors, and fruit texture. This work demonstrates yet again the utility of the differential display technique to rapidly identify genes related to desirable traits.