The genetic improvement of local chicken breeds is essential for sustainability and adaptability. Marker-assisted breeding can increase the response to selection; however, it requires the identification of marker associations with different traits. Therefore, the current study aimed to evaluate the association between microsatellite marker alleles and the body weight of juvenile chicks over three subsequent generations. Ten microsatellites were used to genotype four chicken lines (two selected and two randombred) across three generations. The lines included the normally feathered selected line (CE1), the normally feathered randombred line (CE2) used as a genetic control for CE1, the naked-neck selected line (CE3), and the naked-neck randombred line (CE4) used as a genetic control for CE3. Seventy-four alleles were detected in the two groups across the three generations. Of these, 22 alleles were selected for association analysis based on their frequency across the subsequent generations. The most important alleles were 419 bp at the LEI0079 locus, 186 bp at the LEI0094 locus, and 118 bp at the ADL0158 locus. The current results also highlight additional promising alleles, such as 231 bp at the LEI0079 locus and 233 bp at the ADL0158 locus. These alleles accumulated in the selected chickens and affected body weight at different ages. The results suggest that these loci contain growth-related genes. These results may enhance the understanding of these regions not only in chickens but also in other domestic animals.