Three Vitis species were used to investigate the effects of sunlight exposure on anthocyanin accumulation in five developmental stages. The berries of these three grapes were treated with exclusion of sunlight or recovery of sunlight during different developmental stages. Vitis labrusca cannot accumulate anthocyanins in its berries under dark conditions. V. acerifolia and V. cinerea can accumulate anthocyanins under dark conditions. Using high-throughput RNA sequencing, we produced transcriptomes for these samples. Then, we constructed a weighted gene co-expression network of these three Vitisspecies and defined 17 modules which were correlated to anthocyanin concentrations, developmental stages and species. Analysis of the anthocyanin correlated co-expression network module revealed that two novel bHLH genes might be involved in anthocyanin regulation in grapes. Moreover, the hormone transductions might enhance anthocyanin accumulation in V. acerifolia and V. cinerea under dark. Further functional analysis of anthocyanin negatively correlated modules revealed that anthocyanin accumulation might be inhibited by COP1-dependent protein degradation before veraison and under dark conditions in grape berries.