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Functional marker (FM) is one of the most useful molecular markers in crop breeding, which facilitates the realization of high-throughput genotyping and marker-assisted selection (MAS). In this study, 22 KASP markers were developed according to the reported functional loci of important traits in soybean, including stem growth habit (Dt1), multi-seed pods (Ln), shattering pods (Pdh1), seed size (GmSSS1, GmST05), flowering time (J, GmPRR3a, GmPRR3b, GmFUL2a, GmLHY1a, GmLHY1b, GmSOC1a, E4), protein and oil content (GmSWEET39), carotene content (GmCCD4), phosphorus use efficiency (GmPHF1), nitrogen use efficiency (GmGLP20.4), symbiotic compatibility in nodulation (Rj2) and cytokinin biosynthesis (GmCXK7-1). All of the 21 markers could be used to accurately classify heterozygous and homozygous genotypes, except that the marker of e4-sore could not distinguish heterozygous samples. Combining with phenotypic information, the selection efficiency of multi-seed pod, leaf shape and stem growth habit markers was analyzed. The results showed that the selection efficiency of multi-seed pod (Ln) markers on phenotype was 84.0%, that on leaf shape was 94.8%, and that of stem growth habit (Dt1) markers on phenotype was 87.4%, showing a high level of selection accuracy. The 22 functional markers developed in this study can be used to accurately identify the genotypes and have important utilization value in marker assisted breeding of soybean. [ABSTRACT FROM AUTHOR]