Nitrogen is a crucial nutrient for soybean growth and production. Enhancing soybean crop yield is essential to address the growing challenge of ensuring food security. While nodulation and nitrogen fixation reduce the need for additional nitrogen, the presence of actively fixing nodules, distinguished by their pink or red color, ensures effective nitrogen fixation and yield improvement in soybeans. Changes in global climate led to shifts in soil characteristics that restrict root growth and create conditions resembling drought, diminishing the capacity of plant roots to absorb water and nutrients, consequently impacting overall plant growth as well as nodulation related traits. In this research, we’re examining nodulation related traits across 500 late maturing soybean accessions. We germinated seeds on germination paper and transferred them to blue blotting papers and captured root images after 21 days. Nodulation traits such as Nodules number and area will be evaluated using the Soybean Nodule Acquisition Pipeline (SNAP). Statistical assessments including population structure, kinship matrix, and principal component analysis will be measured using R. We’ll utilize both phenotypic data and SNPs from Illumina Infinium SoySNP50K iselect SNP Beadchip for Genome-wide Association Studies (GWAS) using the GAPIT package in R. This study aims to identify genetic regions linked to nodulation traits, potentially uncovering valuable QTLs or genes for enhancing nodulation related traits.