ABSTRACT Macamides and Macaenes are the bioactive marker compounds in maca (Lepidium meyenii Walp., Brassicaceae) tuber. To simultaneously quantify these two types of compound, HPLC method was studied. To distinguish and group the growing regions of different maca samples, Hierarchical cluster analysis, a chemometric method, was applied to analyze the HPLC data. The calibration curves obtained using the HPLC method showed satisfactory linearity with determination coefficients >0.9998. The precision and repeatability relative standard deviation values were <4%, and the accuracy relative standard deviation value was <5%. The limits of detection was <0.1 µg/ml and the limit of quantification was <0.3 µg/ml. Our HPLC method was successfully used for the separation and determination of macamides and macaenes in Maca within 45 min, i.e., two macaenes (9-oxo-10E,12Z-octadecadienoic acid and 9-oxo-10E,12E-octadecadienoic acid) and five macamides (N-benzyl-9-oxo-10E,12Z-octadecadienamide, N-benzyl-9-oxo-10E,12E-octadecadienamide, N-benzyl-9Z,12Z,15Z-octadecatrienamide, N-benzyl-9Z,12Z-octadecadienamide and N-benzyl-hexadecanamide). The HPLC method was applied to analyze and quantify the seven compounds in thirty maca samples with different colors and origins. The origins of all the maca samples were distinguished and grouped using hierarchical cluster analysis of the HPLC data. Accordingly, the metabolism of macaenes and macamides in maca post-harvest processing has also been proposed. The HPLC method is efficient to simultaneously quantify the macamides and macaenes in maca. Analyzing the HPLC data using hierarchical cluster analysis can distinguish maca growing origins.