Lepidagathis Willd., a genus belonging to the Acanthaceae family, is primarily distributed in tropical and subtropical regions worldwide, encompassing approximately 153 species. While considerable morphological research has been conducted on Lepidagathis, it has not completely dispelled taxonomic ambiguities and conflicting interpretations. Molecular analysis emerges as a valuable tool for resolving these taxonomic uncertainties, but the availability of nucleotide sequence data for Lepidagathis has been limited thus far. This study delivers a phylogenetic analysis of Lepidagathis species, utilizing both chloroplast and nuclear regions. The results of Bayesian Inference and Maximum Likelihood phylogenetic analyses consistently segregate the studied Lepidagathis species into two principal clades, denoted as Clade A and Clade B. Notably, this analysis firmly positions the Indian endemic Lepidagathis within Clade A, supported by robust statistical evidence. Furthermore, our biogeographical analysis strongly suggests that the origin of Lepidagathis might be traced back to Eurasia. This research establishes a foundational molecular phylogeny of Lepidagathis, offering valuable insights for future taxonomic investigations. Additionally, it sheds light on the evolutionary history and biogeographical origins of the Lepidagathis genus.