Global food security is endanged by various factors, with one of the most significant being the quantitative and qualitative increase in agricultural production. Given the vital role of rice in the daily nutrition of Iranians and the necessity to enhance the efficiency of limited land resources, it is imperative to increase the yield per unit area. Identifying genotypes carrying alleles of genes associated with grain yield improvement is one of the methods to breed rice plant. Therefore, breeding rice genotypes can be used in breeding programs, to produce high-yield varieties. Given the importance of the number of grain per panicle and its impact on increasing rice grain yield per unit area, this study aimed to screen rice genotypes using a functional marker associated with the Gn1a gene, among several genes related to yield. In this research, 52 localraces and improved genotypes of rice were obtaied from the collection of the Rice Research Institute of Iran. The grain number trait was evaluated based on phenotypic and molecular evaluations in the field related to the band pattern amplified by gene specific primer pairs for Grain number 1a gene (Gn1a), controlling the grain number trait. The genetic evaluation identified 15 cultivars with the allele associated with a large panicle (more than 121 grains per panicle) and 37 cultivars without this allele. This finding, confirmed by phenotypic evaluation, demonstrates the reliability and accuracy of the marker used to predict and differentiate cultivars for upcoming breeding programs. The logistic regression results also supported this outcome. However, several other examined samples exhibited a high number of seeds, indicating the presence of additional genes influencing the seed count per panicle in those lines.