AbstractNear‐infrared reflectance spectroscopy (NIRS) was used to estimate the fatty acid composition of the oil in intact‐seed samples of Ethiopian mustard (Brassica carinata Braun) within a mutation breeding program that produced seeds with variable fatty acid compositions. Five populations, from 1992 to 1996 crops, were included in this study; and NIRS calibration equations for major fatty acids (palmitic, stearic, oleic, linoleic, linolenic, eicosenoic, and erucic) were developed within each single population. Furthermore, global calibration equations, including samples from the five populations, were developed. After external validation, the NIRS technique permitted us to obtain a reliable and accurate nondestructive estimation of the fatty acid composition of the oil, especially for the major acids—oleic, linoleic, linolenic, and erucic. For these, the r2 in external validation was higher than 0.95 by using both single‐and multipopulation equations, and higher than 0.85 for the remaining fatty acids. Moreover, the multipopulation equations provided an accurate estimation of samples from a population not represented in the calibration data set, with values of coefficient of determination in validation (r2) from 0.80 (palmitic and eicosenoic acids) to 0.97 (erucic acid). The ability of NIRS to discriminate among different fatty acid profiles was mainly due to changes within six spectral regions, 1140–1240, 1350–1400, 1650–1800, 1880–1920, 2140–2200, and 2240–2380 nm, all of them associated with fatty acid absorbers. Thus, NIRS can be used to estimate the fatty acid composition of Ethiopian mustard seeds with a high degree of accuracy, provided that calibration equations be developed from calibration sets that include large variability for the fatty acid composition of the oil.