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Pterodon pubescens is a native Brazilian species typical of the cerrado biome, belonging to the Leguminosae-Papilionoideae (Fabaceae) family and popularly known as sucupira branca or faveiro. Its seeds exhibit different integument colors, which may exhibit a direct association to physiological quality related to higher germination percentage rates, vigor, and germination speed index (GSI). Therefore, selection and evaluation methods concerning P. pubescens seed quality are required for the preservation of this species. In this context, the aim of the present study was to determine the relationship between P. pubescens seed integument color and seed quality, through a combination of radiographic imaging and physiological, histochemical and biochemical assays. P. pubescens seeds were obtained from five matrices, and visually classified into four color classes, yellow, light brown, dark brown and black. The coordinates “L”, “a” and “b”, indicated by the colorimeter and the calculations of the chroma and hue angle values, verified that there was a difference in the color of the seeds, eliminating the subjectivity of the visual classification. Thus, the clearer the integuments, the greater their density, filling and α-amylase and β-amylase hydrolytic enzyme activities, the latter comprising important germination power indicators, in addition to high ascorbate peroxidase (APX) enzyme activities, responsible for hydrogen peroxide (H₂O₂) elimination. Because of this, lighter colored seeds led to higher vigor, germination and GSI rates. The removal of darker seeds from P. pubescens seed lots guarantees higher germination rates and vigor of new plants in nurseries destined to recompose P. pubescens populations. Full article