This study aimed to determine the genetic diversity among 18 soybean (Glycine max L.) genotypes (13 breeding lines and 5 commercial varieties). For this purpose, a total of 36 SCoT (Start Codon Targeted) primers were screened in the samples and 12 primers showing high levels of polymorphism were selected for further analysis. PCR amplification using these primers yielded 115 scorable bands, 83 of which were polymorphic, resulting in a high polymorphism rate of 72.18%. With their high polymorphism rates and PIC values, SCoT-6 and SCoT-26 stand out as suitable for evaluation in breeding applications such as parental selection. The generated UPGMA dendrogram divided the genotypes into two main clusters. In particular, the G-3 genotype exhibited the lowest similarity (0.571) compared to G-14, indicating that this genotype could be a genetically distinct resource for expanding the breeding pool. In contrast, the G-10 and G-11 genotypes exhibited the highest genetic similarity (0.923), reflecting their similar genetic background. Principal Component Analysis (PCA) and Clustering (UPGMA) results were found to be mutually supportive. The observed genetic variation within and between groups demonstrates the effectiveness of SCoT markers in distinguishing soybean genotypes and highlights the presence of diverse allelic sources. These findings provide valuable molecular information for sustainable soybean breeding efforts aimed at improving parental selection, heterotic group formation, productivity, adaptation, and genetic resistance.