Phylogenetic analyses of Avicennia species have been carried out using diverse molecular datasets, including chloroplast genome sequences and multilocus nuclear gene markers. These studies have contributed valuable insights into evolutionary relationships within the genus and clarified its placement in the Acanthaceae family. Concatenated sequence datasets provide broader genomic information and can enhance the resolution and reliability of phylogenetic trees. In parallel, the multispecies coalescent (MSC) model offers a robust framework for addressing evolutionary questions such as estimating species divergence times, population sizes, species tree topologies despite gene tree discordance, interspecific gene flow, and species delimitation.The genus Avicennia L., comprising approximately eight species, represents a key group of mangrove plants, some of which occur along the southern coasts of Iran. However, considerable uncertainty remains regarding the molecular phylogeny of these species. Therefore, this study applies both MSC-based and concatenation-based phylogenetic approaches to investigate species relationships within Avicennia, using molecular data from nuclear ITS and chloroplast psbA sequences. We constructed species trees using BEAST (StarBEAST), performed gene-based analyses in Mesquite, and generated maximum likelihood trees. The results revealed two major divergent clades, with evidence of deep coalescence, interspecific introgression, and structural DNA variations, suggesting a complex evolutionary history within the genus.
