Flowering time is a key agronomic trait that directly influences the successful adaptation of soybean ( Glycine max) to diverse latitudes and farming systems. Gm FT2a and Gm FT5a have been extensively identified as flowering activators and integrators in soybean. Here, we identified two quantitative trait loci ( QTLs) regions harbouring Gm FT2a and Gm FT5a , respectively, associated with different genetic effects on flowering under different photoperiods. We analysed the flowering time of transgenic plants overexpressing Gm FT2a or Gm FT5a , ft2a mutants, ft5a mutants and ft2aft5a double mutants under long‐day ( LD) and short‐day ( SD) conditions. We confirmed that Gm FT2a and Gm FT5a are not redundant, they collectively regulate flowering time, and the effect of Gm FT2a is more prominent than that of Gm FT5a under SD conditions whereas Gm FT5a has more significant effects than Gm FT2a under LD conditions. Gm FT5a , not Gm FT2a , was essential for soybean to adapt to high latitude regions. The ft2aft5a double mutants showed late flowering by about 31.3 days under SD conditions and produced significantly increased numbers of pods and seeds per plant compared to the wild type. We speculate that these mutants may have enormous yield potential for the tropics. In addition, we examined the sequences of these two loci in 202 soybean accessions and investigated the flowering phenotypes, geographical distributions and maturity groups within major haplotypes. These results will contribute to soybean breeding and regional adaptability.