Anthocyanins, a class of flavonoid compounds that provide pigmentation to plant organs, are beneficial components of the human diet and there is an interest in understanding the regulation of their formation in crop plants. The apple cultivar\'May\' represents an excellent model for the study of anthocyanin metabolism due to the spatial color pattern of its flesh, which transitions sequentially from red to white to red again, from the outside to the inside of the apple fruit. To screen the transcription factors involved in the anthocyanin pathway, transcriptomes from differently colored sections of\'May\' fruits were analyzed by RNA sequencing. Kyoto Encyclopedia of Genes and Genomes (KEGG) database was used to analyse the gene expression data. The results suggested differentially expressed genes (DEGs) that are related to phytohormones are involved in regulating anthocyanin biosynthesis. K-means clustering analysis revealed 167 common DEGs between different sections of fruit with the same expression pattern as candidates for regulating anthocyanin synthesis. Further analysis showed that nine of the 167 DEGs were annotated as transcription factors and quantitative real time PCR (qRT-PCR) confirmed that their expression was obviously higher in red regions of the fruit, consistent with their roles as hub genes that regulate anthocyanin synthesis. This study provides valuable results for future studies of anthocyanin synthesis in apple fruit.