This study is the first report on the composition and variability of essential oil in the relic, endemic, and vulnerable tree species Serbian spruce, Picea omorika, in its natural populations. In the needles of 108 trees of four natural populations, 49 components of essential oils were identified. The main compounds were bornyl acetate (29.2%), camphene (18.7%), and alpha-pinene (12.9%). Fourteen additional components had the contents of up to 0.5%: alpha-cadinol (6.1%), limonene (5.8%), santene (3.5%), (E)-hex-2-enal (2.9%), T-cadinol (2.9%), delta-cadinene (2.3%), tricyclene (2.1%), myrcene (1.6%), beta-pinene (1.2%), borneol (0.9%), germacrene D (0.9%), alpha-muurolene (0.6%), and two unidentified compounds. Population IV from Milesevka Canyon had a much higher content of bornyl acetate (42.9%). Populations I-III from Mt. Tara were more abundant in sesquiterpenes (up to 18.2%). The content of bornyl acetate, the multi-variation analyses according to seven selected components, especially the cluster analysis and genetic analysis of alpha-cadinol, which suggested the monogenic type of heredity, showed a clear differentiation of the two geographic areas, the similarity of populations I-III from the area of Mt. Tara, and the separation of the population IV from Milesevka Canyon.