The phenolic compounds and anthocyanins present in myrtle berries are responsible for its beneficial health properties. In the present study, a new, microwave-assisted extraction for the analysis of both phenolic compounds and anthocyanins from myrtle pulp has been developed. Different extraction variables, including methanol composition, pH, temperature, and sample⁻solvent ratio were optimized by applying a Box⁻Behnken design and response surface methodology. Methanol composition and pH were the most influential variables for the total phenolic compounds (58.20% of the solvent in water at pH 2), and methanol composition and temperature for anthocyanins (50.4% of solvent at 50 °C). The methods developed showed high repeatability and intermediate precision (RSD < 5%). Both methods were applied to myrtle berries collected in two different areas of the province of Cadiz (Spain). Hierarchical clustering analysis results show that the concentration of bioactive compounds in myrtle is related to their geographical origin.