The threatened and endangered species distribution data are frequently clustered, and modeling their suitable habitat distribution by commonly utilized modeling methods is difficult. Therefore, this work aimed to assess the potential geographic distribution of Nepeta septemcrenata and Phlomis aurea in the St. Katherine protectorate using a new maxent approach. In addition to identifying the principal environmental parameters, which highly affect the potential geographic distribution of Nepeta septemcrenata and Phlomis aurea in the St. Katherine protectorate. The findings presented that the assessment distribution of Nepeta septemcrenata and Phlomis aurea is concentrated in the high-mountain region in SKP. While the driest quarter's precipitation, the coldest quarter's precipitation, the warmest quarter's mean temperature, the coldest quarter's mean temperature, and elevation all had a role in Nepeta septemcrenata distribution. The coldest quarter's mean temperature, the driest quarter's mean temperature, precipitation seasonality, the warmest quarter's mean temperature, all had a role in the distribution of P. aurea. Additionally, the highly suitable ecological conditions for Nepeta septemcrenata cover about 200.5 km2 from the total protectorate area, while the highly suitable ecological conditions for Phlomis aurea cover only 104.1 km2. This work may help in conservation planning for these threatened and endemic species.