Shada Mountains in Saudi Arabia, separated by Maleel Wadi into twin mountains (i.e., Shada Alalah and Shada Asfal), are rich in biodiversity. We investigated the diversity of endemics and endangered species of the mountains based on the data collected from 38 stands falling in 8 elevational zones ranging from 500 to 2215 m a.s.l. Results indicated that 495 plant species falling in 314 genera and 76 families occurred in the Shada Mountains, including 19 endemic species and 43 endangered species, and accounting for 22% of the total flora in Saudi Arabia. Canonical correlation analysis indicated that physiographic features, particularly altitude play an important role in the frequency and abundance of species. Endemics were not evenly distributed in the Shada Mountains and mostly restricted in the elevation zone of 1000-1500 or >1500 m a.s.l. When the altitude reached up to 2000 m a.s.l., the endemics decreased substantially due to the significantly low temperature. The endangered species existed three different distribution patterns: (i) most endangered species distributed in the altitudes of 1000-1800 m a.s.l.; (ii) endangered trees, lianas, and shrubs occupied the altitudes 1000-1300 m a.s.l.; and (iii) endangered subshrubs and herbs inhabited the altitudes 1500-2100 m a.s.l. The results demonstrated that the biodiversity of endangered species in the Shada Mountains is high and undisturbed by invasive species, and protective measures should be taken against human disturbances to the small-scale hotspot.