The present study aimed to identify molecular markers associated with long juvenility and photoperiod insensitivity in soybean. F₃ segregants from three crosses MAUS 71 × AGS 25, MAUS 612 × AGS 25, and PP6 (EC 390977) × 291133 (EC 538828) were evaluated through both morphological and molecular analyses to validate loci responsible for these traits. Bulked segregant analysis (BSA) was employed to detect and confirm markers linked to photoperiod insensitivity and long juvenility. The long juvenile trait was successfully tagged with SSR markers Satt197 and Satt063 in late-sown F₃ segregants, providing useful tools for marker-assisted selection in soybean breeding programs.