Lepidagathis Willd., a genus belonging to the family Acanthaceae, is present pantropically and consists of about 151 species. Classification of Lepidagathis and Lophostachys has been under debate for a long period. Earlier, they were separated based on their distribution and morphology. However, according to Benoist 1911, the morphological differences were very slight; hence, both were considered under the genus Lepidagathis. Molecular analysis is the most effective method to clear up taxonomic issues, but more data is needed regarding Lepidagathis and Lophostachys. Lepidagathis cristata, the type species of this genus, has no molecular sequences available. Therefore, the purpose of this study was to sequence several plastid markers, which are frequently employed for the phylogeny of Acanthaceae and species DNA barcoding. Subsequently, phylogenetic trees using Bayesian and maximum likelihood bootstrap methods were built. The predominantly Asian species formed a clade which we characterize as Lepidagathis s.s was found monophyletic with strong Bayesian posterior probability support as well as good maximum-likelihood bootstrap support. Lepidagathis s.s was sister to another well-supported clade consisting of the genus Lophostachys. This phylogenetic study, along with the biogeographical distribution proves that Lepidagathis and Lophostachys are independently evolving clades, which can be treated as different subgenera.