Rapanea ferruginea Mez. stem barks and fruits extracts have demonstrated anticholinesterasic and antimicrobial activities assigned to myrsinoic acids A and B (MAA and MAB), compounds that have also proven anti-inflammatory and antinociceptive activities. To stablish the quality control of nanotechnology-based herbal medicines, the aim of this study was develop and validate a stability indicating HPLC-DAD method for quantitative analysis of MAA and MAB markers in R. ferruginea stem barks and fruits extracts and nanoemulsions. Chromatographic separation was conducted on a Kinetex ® C 18 column (150 x 4.6 mm x 2.6 µm), with mobile phase consisted of acetonitrile: methanol: water (acidified with H 3 PO 4 pH 2.50) and eluted in gradient mode with flow rate of 0.9 mL min-1 , with 30 min of analysis and detection at 260 nm and 270 nm. The method was specific, linear, sensitive, accurate and robust for both markers. The chromatograms of stem barks and fruits extracts submitted to forced degradation study (acid, oxidative, UV and visible light) did not show impurities interference in MAA and MAB quantification, therefore, the method was considered stability indicative. The developed method has been successfully used to quality control of R. ferruginea extracts and nanoemulsions containing these extracts and applied to the stability study of nanoemulsions.