Lippia origanoides Kunth. is a medicinal shrub native to some countries in South America, Central America and the Caribbean. This study aims to investigate the chemical composition of the essential oil and the genetic diversity of a natural population of Lippia origanoides in two seasons. Leaf samples were collected from 30 individuals in the dry and rainy seasons. The essential oil was extracted into a Clevenger apparatus and analyzed by gas chromatography coupled to mass spectrometry (GC-MS). The relative quantification of thymol and carvacrol was performed by gas chromatography coupled to a flame ionization detector (GC-FID). Multivariate analysis was used to evaluate the genetic divergence between plants. Carvacrol was the major compound found in most plants for both seasons. In the rainy season, plant 15 presented thymol as the major compound, and plants 16, 27, 28 and 29 presented camphor as the major compound. In the dry season, thymol remained the main compound of plant 15 and camphor remained the main compound of plants 16, 28 and 29; however, plant 27 presented carvacrol as the main compound in this season. After carvacrol, the compounds with the highest content were γ-terpinene, p-cymene and methyl-ether-thymol. Of the 30 plants studied, only five differed in their chemical composition, showing some degree of stability in relation to the dry and rainy seasons. There was no variation in the main compounds between the two seasons, but there was chemical diversity among the main compounds. Tocher grouping revealed five distinct groups, with group 1 including most of the plants in both dry and rainy seasons, indicating that the time of year evaluated did not significantly interfere with the essential oil composition of most plants.