Nepeta binaludensis Jamzad is an endemic and rare perennial plant belonging to the Lamiaceae family, which grows in a limited area in Binaloud Mountain in northeast of Iran. In this study to evaluate the diversity of 20 populations (localities) of N. binaludensis and the influence of environmental factors on essential oil (EO) content and composition, the plant aerial parts were collected at the full flowering stage. The plant materials dried in shade and subjected to hydro-distillation for obtaining their EOs. Analysis of the EO was carried out using GC and GC/MS. The oil yields were varied from 1.2 to 4.9%. Classification of populations was made based on EO compounds. The results of mean comparison between populations belong to different habitats showed that the populations of Darood and Friezy with average values of 4.91 and 1.2% had the highest and lowest EO yield, respectively. Twenty-two compounds were identified in the oils with 1,8-cineol (25.4–59.0%), 4aα,7α,7aα-nepetalactone (13.8–55.1%), myrcene (2.3–5.5%) and p-cymene (1.1–5.7%) as the main components. Result of correlation analysis showed that the oil yield was positively correlated with precipitation and negatively with temperature. In addition, 1,8-cineole was positively and nepetalactone was negatively correlated with altitude. Cluster analysis by Ward method categorized the populations into two groups. The major compound of the oils in cluster 1 was nepetalactone (with an average of 37.9%), while the oils in cluster 2, contained higher percentage of 1,8-cineole (52–59%). Most of the populations in cluster 2, were originated from high, cold, rainy, and steep areas.