Propolis is produced by the honeybees by using resin and other plant secretions. Propolis from different geographical regions have different chemical compositions. This is because the chemical constituents of propolis depend on the vegetation surrounding the apiary. In this report we present a new approach using DNA barcoding for the identification of the botanical origin of propolis. Red propolis samples were collected at different times of the year from the state of Sergipe situated in Northeast Brazil. Extraction of the DNA from propolis was made using a CTA B method. Amplification was done using ITS 2 universal primers, followed by DNA sequencing. Sequence analysis confirmed the presence of Dalbergia ecastaphyllum in the Brazilian red propolis. Formononetin is a chemical marker for the Brazillian red propolis and D. ecastaphyllum. Propolis samples analysed by DNA sequencing, were also checked by Ultra-Fast Liquid Chromatography for the presence of formononetin. Peaks corresponding to formononetin were observed in all the analysed propolis samples. This is the first report of the botanical origin of propolis using DNA technology.