Myrtle (Myrtus communis L., Myrtaceae) has numerous applications in pharmacology, food technology, and cosmetic industry. The current research aimed at measuring variations in the leaf essential oil (EO) compositions of 14 superior myrtle accessions originating in natural habitats of south Iran. The plants were grown under greenhouse conditions. Fresh leaf samples were harvested in June 2021. Based on dry matter, the extractable amount of EO in the accessions ranged from 0.42% (BN2) to 2.6% (BN5). According to GC/MS analysis, the major compounds in the EO were α-pinene (2.35–53.09%), linalyl acetate (0–45.3%), caryophyllene oxide (0.97–21.8%), germacrene D (0–19.19%), α-humulene (0–18.97%), 1,8-cineole (0–18.0%), limonene (0–17.4%), and p-cymene (0–13.2%). These myrtle accessions were classified into four groups, including I: caryophyllene oxide/germacrene D/α-humulene/methyl eugenol chemotype; II: α-pinene/p-cymene/α-humulene and (E)-β-caryophyllene; III: α-pinene/1,8-cineole, and linalool; IV: linalyl acetate/γ-terpinene/1,8, cineole/limonene. These classifications were established by considering the main EO components using hierarchical cluster analysis (HCA) and principal component analysis (PCA). In summary, this study provided new insights into available opportunities of selecting suitable genotypes for commercial cultivation purposes and planning breeding programs in the future.