Molecular markers associated with soybean reproductive stage, methods of their use, and compositions having one or more marker loci are provided. Methods comprise detecting at least one marker locus, detecting a haplotype, and/or detecting a marker profile. Methods may further comprise crossing a selected soybean plant with a second soybean plant. Isolated polynucleotides, primers, probes, kits, systems, etc., are also provided, as well as plants and seeds comprising one or more marker loci and having a preferred reproductive growth phenotype.