Kanihua and quinoa are closely related Andean grains that are unconventional starch sources. Starch was extracted from two kanihua and three quinoa genotypes and their physicochemical properties (proximate analysis, scanning electron microscopy, distribution and particle size, X-ray diffraction, FTIR, solubility, swelling power, pasting and thermal properties) were investigated. Kanihua and quinoa grains presented spherical shapes and regular sizes (1.05 - 1.30 mm). The starch granules show asymmetric monomodal distribution for all cases. Meanwhile, Sauter diameter values in kanihua were smaller (0.961 µm) than quinoa (1.099 µm). Regarding structure, all samples showed Type A polymorphism and similar FTIR spectra behavior. In addition, amilose content was around 11-14% and 8-12% for varieties of kanihua and quinoa respectively. Starch solubilities were less than 13%, and kanihua starches had less swelling power than quinoa starches. However, the maximum swelling power values were reached around 70 °C. The variety and type of grain influenced pasting properties, with an inverse relationship between the breakdown and setback values for the evaluated starches. Analyzing the thermal properties, gelatinization enthalpy and retrogradation were similar for all starches. Even though the kanihua and quinoa starches present similar structural characteristics, the pasting properties and swelling power were different. The insight into the morphological, thermal, and pasting properties of native Chenopodium starches could be helpful in the preparation and development of new food formulations.