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Hesperozygis ringens Benth. (Lamiaceae) is an aromatic and medicinal plant, characterized by a high concentration of isopulegone; it is endemic to the mountains of southeast Rio Grande do Sul, Brazil, and currently is considered endangered. The present study evaluated the intra- and interpopulation genetic variability of H. ringens by means of RAPD and ISSR molecular markers. The results showed that H. ringens populations are genetically structured, with low gene flow between populations, confirming the fragmentation imposed by anthropic action. Populations from the two areas of occurrence are genetically different. Low intrapopulation variability and heterozygosity were detected, indicating genetic drift and inbreeding. Based on the data, conservation strategies are discussed.