|Sorghum bicolor (L.) Moench) is a cereal consumed all over the world especially in arid and semi-arid areas where it is a staple food. It is also used as fodder for animals in the developed countries and also as a merging biofuel source. Sorghum bicolor shows lower protein digestibility as the major nutritional constraint to the consumers. Natural variation for the protein digestibility exists and the aim of this study was to determine the genetic determinants that influence protein digestibility among selected Sorghum multi-parent advanced generation intercross (MAGIC) lines which were generated after multiple crosses with nineteen founder parents and ten Checks in addition. Total protein/crude protein was determined using the micro Kjeldhal method and pepsin test. The IVPD was obtained as a difference between the crude and what was left after pepsin digestion expressed as a percentage. One hundred and seventy-seven genotypes had the marker data as well as the protein data and were thus considered for the study. The analysis of variance (ANOVA) revealed significant differences in digestibility among the genotypes tested at (p < 0.05). MAGIC lines M171, M189, M188, M053 and M178 had the highest stable protein digestibility at 87%, 84%, 80%, 80% and 78% respectively. M153, M029 and M140 had the lowest digestibility at 4%, 17% and 20% respectively. Among the checks, SEKEDO had 78% protein digestibility, lower than M171 and M189, the two best MAGIC lines. Genome wide association study was conducted in TASSEL using 45,120 filtered SNPs out of 79,000 SNPs obtained via Genotyping-by-sequencing (GBS). Manhattan plots for Crude protein (CP), in vitro protein (IVP) and protein digestibility (PD) were obtained with significant peaks on chromosomes, one, three, four, and nine based on the general linear model (GLM). Seven SNPs were associated to CP and IVP, and these includedS1_10455978, S1_104560000, S1_207581014, S1_217853008, S1_280568282, S1_594605714 and S1_594605757. The SNP S1_280568282 at 54.7 Mb was detected near nitrate reductase (NR) 1 gene that catalyzes the first reaction in nitrate assimilation reducing nitrate to nitrite then to ammonia and finally to nitrogen which is key in amino acid formation. In addition to the other QTLs associated to the candidate genes, marker assisted selection for the trait can be employed and new breeder lines acquired.