TheZiziphus mauritianaLam. andZ. jujubaMill. are the two most economically important members of the genusZiziphus.The fruit color ofZ. mauritianaremains green throughout fruit development in the majority of commercial cultivars, whereas its close relative,Z. jujubaMill. turns from green to red in all cultivars. However, the lack of transcriptomic and genomic information confines our understanding of the molecular mechanisms underlying fruit coloration inZ. mauritiana(Ber). In the present study, we performed the transcriptome-wide analysis of MYB transcription factors (TFs) genes inZ. mauritianaandZ. jujuba, and identified 56 ZmMYB and 60 ZjMYB TFs inZ. mauritianaandZ. jujuba, respectively. Through transcriptomic expression analysis, four similarMYBgenes (ZmMYB/ZjMYB13, ZmMYB/ZjMYB44, ZmMYB/ZjMYB50, andZmMYB/ZjMYB56)fromZ. mauritianaandZ. jujubawere selected as candidate key genes regulating flavonoid biosynthesis. Among these genes, theZjMYB44gene was transiently highly expressed in fruit, and flavonoid content accumulation also increased, indicating that this gene can influence flavonoid content during the period of fruit coloration inZ. jujuba. The current study adds to our understanding of the classification of genes, motif structure, and predicted functions of the MYB TFs, as well as identifying MYBs that regulate flavonoid biosynthesis inZiziphus(Z. mauritianaandZ. jujuba). Based on this information, we concluded thatMYB44is involved in the flavonoids biosynthesis pathway during the fruit coloring ofZiziphus. Our research results provide an important understanding of the molecular mechanism of flavonoid biosynthesis resulting in fruit coloration and laying a foundation for further genetic improvement of fruit color inZiziphus.