Chickpea (Cicer arietinum L.) is one of the most important food legume crops consumed by human beings and can be used to counteract specific dietary deficiencies. Protein, lutein, vitamin C, and fructose are among the important nutritional value components of chickpea. The objectives of this study were to determine genetic variation in the concentrations of nutritional value components in the seeds of cultivated Cicer arietinum and its wild progenitor Cicer reticulatum Ladiz. and detect single nucleotide polymorphism (SNP) markers associated with these concentrations. A representative population of 180 Cicer genotypes from the two species was evaluated in two locations in Turkey in 2 yr, and the population was genotyped using 121,840 SNP markers obtained using the genotyping-by-sequencing analysis. The associations between the nutritional value components and loci were investigated in TASSEL software using the mixed linear model method through three different analyses. A considerable SNP stability was observed between the different year-site replicates, and 29, 10, 14, and 4 SNPs were significantly associated with protein, lutein, vitamin C, and fructose, respectively. This study provides an understanding of the genetic basis of variability in the seed concentrations of nutritional value components in chickpea. The identified markers can be used for marker-assisted selection to improve the nutritional value components of chickpea in biofortification programs.