One of the key challenges in aquaculture is the selection of individuals with superior traits, including rapid growth rate, high flesh quality, and disease resistance. Marker-assisted selection (MAS) using molecular markers (e.g., simple sequence repeats; SSR) is known to be more effective in identifying individuals with specific traits based on their genetic makeup. The current study aimed to examine SSR markers across different linkage groups in their efficiency in characterizing the Nile tilapia fish with superior growth performance traits for usage as effective tools for MAS. A total of 152 Nile tilapia samples with identical ages but contrasting growth performances were collected from a fish farm in Kafr El-Sheik Governorate, Egypt. The collected genotypes were evaluated for growth performance metrics such as weight and length, and their microsatellite allelic patterns were also analyzed. A total of 13 microsatellite markers were assessed in the two sampled Nile tilapia categories. The t-test of growth performance traits between the two fish categories revealed highly significant differences in body weight and length. The average number of alleles per locus in the large and small populations was 2.6 and 2.2, respectively. The analyzed populations showed a significant deviation from Hardy-Weinberg equilibrium.Only seven markers showed private alleles unique to either small or large populations, indicating the suitability of these markers for association genetic studies. The studied markers showed low to moderate gene diversity (H), which ranged between 0.25 and 0.48, with an average of 0.41. The discrimination power of the studied loci was relatively high (D = 0.888). The discrepancies in growth parameters between the investigated populations were aligned with the disparities in allele frequency, indicating a possible correlation between certain allele(s) and growth performance characteristics. The present study highlighted the effectiveness of specific SSRs in addressing growth parameters during the planning for the Nile tilapia selection in breeding programs.