Moringa (Moringa oleifera Lam. - Moringaceae) is a plant originating in India, which has been widely cultivated in different regions of the world, especially due to the nutritional properties of its leaves, which are of high economic, medicinal and industrial interest. However, there are no reports on the genotypic and phenotypic diversity of moringa seedlings cultivated in the Central-West region of Brazil. This study aimed to characterize a population of moringa seedlings using different qualitative morphological descriptors. A population consisting of 1,263 28-day-old moringa plants was initially classified and separated into four distinct phenotypic groups based on hypocotyl color [seedlings with hypocotyls colored green (100% green), ¾ green (75% green and 25% purple ), ¾ purple (25% green and 75% purple), and purple hypocotyl (100% purple)]. Initially, the seedling emergence rate and the frequency of occurrence of the different hypocotyl color classes in the total population were evaluated. Subsequently, 10 morphological descriptors were evaluated in each group of plants with different hypocotyl color. The plant emergence rate was 74%, indicating the adequate physiological quality of the seeds. The separation of the population into four phenotypic groups based on the color of the hypocotyl allowed us to separate 432 plants (34.2%) with a green hypocotyl, 480 plants (38.0%) with a ¾ green color, 336 plants (26.6% ) ¾ purple in color and 15 plants (1.2%) with purple hypocotyls. The results reported that of the ten morphological descriptors evaluated, only the type of insertion of the first pair of leaves (TI_1F) and the height of insertion of the first leaf (AI_1F) have significant differences (P < 0.05) between the different phenotypic groups of seedlings. moringa. Seedlings from the phenotypic group with purple or ¾ purple hypocotyls have the entire insertion of the first pair of daughters of the opposite type, while seedlings with green and ¾ green hypocotyls have, respectively, 25% and 42% of the plants with the insertion of the first pair of alternating leaves. Seedlings with purple hypocotyls have a higher insertion height of the first leaf (AI_1F) when compared to green and ¾ green seedlings. Highly significant and negative correlations were obtained between TI_1F and DC (–0.99, P < 0.05) and VR (–0.96; P < 0.05). Highly significant and positive correlations were obtained between AI_1F and DC (0.96; P < 0.05). It can be stated that there is genetic and phenotypic variability within a population of moringa seedlings, and the distinct phenotypic groups separated based on hypocotyl color have some characteristics or morphological descriptors typical of their group.