Genus Morus (Family Moraceae) comprises 13 species of mulberries distributed throughout temperate and subtropical regions of the world. Morus rubra, also known as red mulberry, is an endangered species native to North America and is found in riparian areas of eastern North America. Species integrity of M. rubra is threatened by introgressive hybridization with its invasive exotic congener M. alba (white mulberry). The interspecific hybridization is believed to pose a challenge of species identification. In order to address this challenge, and threats posed by hybridization to the species integrity of M. rubra, we conducted an analysis of chloroplast genomes of M. rubra, M. alba and hybrid individuals. The M. rubra chloroplast genome is 159,421 bp with 128 genes that code for 83 proteins, 8 ribosomal RNAs (rRNAs), and 37 transfer RNAs (tRNAs). Analysis of the genome size, GC content, and pattern of simple sequence repeats (SSRs) revealed a high degree of similarities between the two species. The chloroplast genome of M. rubra is larger than that of M. alba by 120 bp. Phylogenomic analysis of the chloroplast genomes of 11 species supported previously published Morus phylogeny with well-resolved Asian and North American clades. Nine hypervariable sites were identified across the genomes, which are yet to be tested for their effectiveness as species-specific markers. The research outcomes of this study not only provide insights into the chloroplast genome structure and organization of M. rubra but also help address taxonomic challenges and serve as an important genomic resource for future studies on Morus species