Mulberry (genus Morus), belonging to the order Rosales, family Moraceae, is an important woody plant due to its economic value in sericulture as well as for its nutritional benefits and medicinal values. However, the taxonomy and phylogeny of Morus remain challenging due to its wide geographical distribution, morphological plasticity, and interspecific hybridization. To better understand the evolutionary history of Morus, we combined plastomes and a large-scale nuclear gene to investigate their phylogenetic relationships in the present study. We assembled the plastomes and screened 211 single-copy nuclear genes from 14 Morus species and related taxa. The plastomes of Morus species were relatively conserved in terms of genome size, gene content and order, IR boundary and codon usage. Using nuclear data, we yielded completely identical topologies based on coalescent and concatenation methods, and multiple individuals of the same species were intraspecific monophyletic. The genus Morus was supported as a monophyly, and M. notabilis was recovered as the first diverging, and the two North American Morus species, M. celtidifolia and M. rubra, were sister to the other Asian species. However, the relationships of Morus based on plastomes were strongly incongruent with those from nuclear genes, and intraspecific non-monophyly was retrieved in the plastid phylogeny. Comparisons of nuclear and plastid phylogenies, and combining with the result of network inference, hybridization/introgression was regarded as the main cause of the discordance between nuclear and plastid phylogenies in the genus Morus. Overall, the robust phylogenetic relationships of Morus described here will be useful for genetic resources development of this economically important genus and exploitation of sericulture industry.