The essential oil from two Lantana species (Lantana lucida Schauer and Lantana salzmannii Schauer) were evaluated for their chemical composition by GC/MS. Results showed 17 predominant compounds for L. lucida, among which (E)-caryophyllene (19.0%) and α-humulene (33.0%) were the major components. L. salzmannii showed the presence of 58 compounds, the most abundant of which were (E)-caryophyllene (15.6%) and selin-11-en-4-ol (11.2%). Next, cluster analyses of the chemical composition of the volatile fraction of five Lantana species from our studies (Lantana radula, Lantana canescens, L. lucida, L. salzmannii and Lantana camara), as well as 10 Lantana species published in the literature (Lantana achyranthifolia, Lantana aculeata, Lantana balansae, Lantana hirta, Lantana involucrata, Lantana fucata, Lantana salviifolia, Lantana trifolia, Lantana velutina and Lantana xenica) were performed. Species fell into three main groups. A cluster analysis of (E)-caryophyllene content was also performed which resulted in the 15 Lantana species being segregated into four main groups. In addition, Inter-Simple Sequence Repeat (ISSR) was used to evaluate the genetic variation between five Lantana species collected from northeastern Brazil (L. radula, L. canescens, L. lucida, L. salzmannii and L. camara). Analysis showed a 36% similarity between, L. salzmanii and L. canescens, and a 48% similarity between L. lucida and L. canescens. Overall, results, indicate that it is possible to discriminate between groups of Lantana taxa based on both their chemical, composition and ISSR markers. In addition, this study provided further support for using (E)-caryophyllene as a chemical marker for species belonging to the Lantana genus.