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Zataria multiflora Boiss. is a rare aromatic species endemic to the southern and southwestern regions of Iran. It is a species that is not under cultivation anywhere else in the world and is only gathered from the wild by amateur collectors. Its cultivation and domestication is very limited. Hence, we investigated the seed germination behaviour and seedling growth of different ecotypes of Z. multiflora collected from 6 sites in Iran (Jam, Ab-garm, Layzangan, Dashte-khak, Kooh-namak, and Chehel-cheshmeh) in late spring. The experiment was carried out at College of Agriculture, Shiraz University, Shiraz, Iran, in 2012. The statistical differences among the ecotypes were determined through variance analysis (ANOVA). The results of the pot experiment showed that ecotype had a significant difference for the total germination percentage, number of leaves per plant, plant height, fresh mass, dry mass, relative water content, and antioxidant enzyme activity. Differences in growth performance were also noted in relation to the altitude of the six test populations: ecotypes at a higher altitude exhibited lower germination rates and plant height. This study is significant for land managers and conservation agencies with an interest in optimizing the germination of arid-zone seeds for rehabilitation of this threatened species.