Denaian thyme, also known as Thymus daenensis (Lamiaceae), is an endangered and endemic medicinal plant in Iran. It is commonly utilized in traditional remedy for its antioxidant, immunomodulatory, and insecticidal effects. The aerial parts of this plant include a variety of bioactive compounds. for instance, flavonoid, phenolic acids, and high levels of terpenoids. until now, wild plants are the primary source of these compounds. However, if harvesting methods are not altered soon, they may become endangered. Alternative production methods for medicinal plants using tissue culture are gaining more interest. no protocol for in vitro culture of T. daenensis has been reported so far. To address this, we carried out a study to investigate the impact of various auxins and cytokinins, both in isolation and in combination, on cell growth, development, and secondary metabolite accumulation. The objective was to assess how certain factors affect the accumulation of phenolic compounds and biomass growth in T. daenensis tissue culture. The response surface methodology modeling outcomes have shown that the use of plant growth regulators (PGRs) and their combinations significantly impacts the in vitro culture of T. daenensis. g plots summarized results showing that the best accumulation of biomass and secondary metabolites can be achieved by using 1-Naphthaleneacetic acid (NAA) followed by 2,4-Dichlorophenoxyacetic acid (2-4-D). Optimizing the induction of secondary metabolites and large-scale biomass production could greatly benefit this species.