The morphometric characterization of watersheds is important because it allows to describe geomorphological processes and infer hydrological behaviors: maximum flows, soil erosion and groundwater recharge. In developing countries, studies on watershed morphometry are scarce; nevertheless, its application is substantial, especially in non-instrumented regions. A morphometric analysis was carried out evaluating the drainage characteristics of two high Andean river basins in the Junin region, Peru: the Anya river basin on the eastern side of the mountain range and the Mchique river on the western flank of the central Andes. The basins were delimited and the morphometric parameters of relief, shape and drainage were calculated, using Geographic Information Systems (GIS). Both basins are of order 3 with differentiated drainage patterns, with the Anya dendritic basin and Mchique subdendritic with influence of structural elements given their particular elongated shape. The low values of drainage density (Dd) fix the basins as having high infiltration rates, however, they respond to their headland locations. The values of elongation (E) imply an elongated shape for Anya and more for Mchique, which indicates a lower vulnerability to flash floods and, consequently, a simpler flood management. The high topographical factor (Ft) of the basins is an indicator of steep slopes and, consequently, of greater intensity of erosive processes. The results can be the basis for hydrological and hydraulic studies, watershed management and water resources management in the area.