LAUSR

ABSTRACT Acanthus ebracteatus is a typical true mangrove species with great ecological and medicinal values. However, it has become endangered in China. Moreover, because of the similar morphology and distribution, it is commonly confused with the congeneric mangrove species, A. ilicifolius, which poses challenges to the protection and proper medicinal utilization of A. ebracteatus. Plastomes provide a solution for molecular identification and adaptive evolution investigation of plants. In this study, we dissected the complete plastome for A. ebracteatus and performed comparative analysis to A. ilicifolius and three non‐mangrove relatives ( A. montanus , A. leucostachyus and A. mollis ). Both plastome sequences and structure are highly conserved between the two mangrove species, while less similar between mangrove and non‐mangrove species. Phylogenetic analysis suggested that the mangrove species were divergent from the non‐mangrove groups at approximately 15.15 million years ago (Mya), where early to middle Miocene global warming and high sea level might act as one of the main forces driving the mangrove lineage entering into intertidal environments. Furthermore, 12 single nucleotide polymorphisms (SNPs) and 10 insertions/deletions (indels) were detected between the plastomes of A. ebracteatus and A. ilicifolius. PCR validation further demonstrated the effectiveness of the plastid marker in distinguishing the two sibling mangrove species. Taken together, our study broadens the understanding of the origin and evolution of Acanthus mangrove plants, and provided valuable information on the correct identification and protection of endangered mangrove species A. ebracteatus .