The large variation in multifactorial and seemingly non-adaptive kernel colour traits displayed by Native American maize landraces is an evidence of recurring selection for perceptual distinctiveness. Native American farmers selected for colour traits that allowed them to distinguish between and maintain large diversity within maize landraces for traditional uses. Multivariate statistical procedures were employed to quantify the variation and interrelationships between physical traits, C:N ratio, protein content, micro- and macronutrient concentrations with kernel colour traits measured on random kernel samples of Northern flint maize landraces grown for 2 years in a common-garden experiment. The colour traits (L*, a* and b* indicating dark–light, red–green and yellow–blue colour continuum, respectively) were digitally quantified on 590 random kernels from each of 28 accessions in 11 landraces. Accessions within landraces exhibited the largest variation for all colour traits. The variation in the L*a*b*, L*a* and L*b* combinations explained significant variances in 37, 14 and 37% of 120 landrace–trait combinations, respectively; the remaining 12% were explained by L*, a* or b*. On average, 37.5% of the variation in protein content (range 19.2–64.5%) and 36.6% of the variation in the C:N ratio (range 15.7–65.0%) were explained by the combinations of colour traits in different landraces. Slightly larger average variations in K (43.7%), S (43.0%), Fe (42.2%) and P (40.8%) were accounted for by colour traits. A hierarchical and joint clustering procedure of landraces and traits was developed to facilitate the identification of large variation and the selection of single or multiple traits based on kernel colour traits with reasonable certainty.