Gynodioecy is a sexual system in which hermaphrodites coexist with females and is frequently observed in Lamiaceae. The aim of this study was to investigate the floral morphology of Elsholtzia angustifolia (Loes.) Kitag (Lamiaceae) using stereomicroscopy (SM), light microscopy (LM), and scanning electron microscopy (SEM) to identify floral dimorphism in a potential gynodioecious species. Two different floral morphs were found in Elsholtzia angustifolia, hermaphroditic and female individuals, from three natural populations in South Korea (Ihwa Pass, Mt. Joryeong, and Mt. Sokli). However, females rarely occur in natural populations. Statistical analysis revealed significant size differences in the floral organs of the floral morphs. Micromorphological and anatomical characteristics were also examined using LM and SEM to compare the differences between the female and hermaphroditic types, revealing significant differences in the stamens between the two sexual types. Additionally, floral scent analysis was performed to identify floral morph-specific scent components, with elsholtzia ketone and dehydroelsholtzia ketone as the major components.