Myrcia ovata Cambess. (Myrtaceae) is a medicinal and aromatic plant that has analgesic, bactericidal and fungicidal properties. Even though this plant has economic potential, nothing is known about the variability and genetic diversity of this species. This information is necessary to establish conservation strategies and allow prospection of natural resources. The aim of this study was to evaluate the genetic diversity of M. ovata individuals of a native population in the municipality of Japaratuba, Sergipe State, Brazil, using Inter-Simple Sequence Repeat molecular markers (ISSR). Nine primers were tested, resulting in 99 polymorphic bands. The 24 individuals evaluated were clustered in two groups by the software Structure. The Jaccard similarity ranged from 0.21 (MYRO-034 and MYRO-159) to 0.82 (MYRO-178.1 and MYRO-178.2), with an average of 0.38. The genetic diversity of M. ovata was considered of medium level. The individuals MYRO-154, MYRO-175 and MYRO- 175.1 presented the most variability.