Magnolia grandiflora is an aromatic plant widely distributed around the world. In Colombia, and more specifically in Bogotá, M. grandiflora has been introduced as part of urban forestry programs, and their specimens are therefore subjected to several environments. Nevertheless, there are no previous studies on the chemical composition of such plants. Hence, the characterization of the essential oil from 20 specimens of M. grandiflora from Bogotá, Colombia, by GC/MS was carried out here. Two different chemotypes were found. While one was characterized by monoterpenes α-pinene, β-pinene, and limonene, the other contained mainly sesquiterpenes β-elemene, bicyclogermacrene, and germacrene D. Multivariate statistical analyses confirmed their existence and helped to identify variations within and between chemotypes. Furthermore, differential expression of genes encoding the terpene synthases Mg25 and Mg17 could arguably be responsible for the characteristic compositions of both chemotypes, as suggested by rational biosynthetic analysis of the most contrasting metabolites.