Soybean （Glycine max （L.） Merr.） is a self-pollinating crop， and producing hybrids through artificial emasculation is time-consuming and expensive. Unlocking the function of the male sterility gene is a prerequisite for harnessing heterosis in soybean. Up to now， only a few loci of male sterility had been reported in soybean， and progress in molecular cloning and functional characterization of related genes lagged behind. Advances in biotechnology and soybean genetic transformation system enabled the possibility to employ reverse genetics methodology for studying the male sterility genes. The transcriptomic data indicated that the small G protein encoding gene GmARFA1a was regulated simultaneously by the male sterility gene MS1 （Male Sterile 1） and MS2. Data from the public library indicated that GmARFA1a expression was the highest in unopened soybean flowers， qRT-PCR data demonstrated that GmARFA1a was preferentially expressed in stamen before flowering. The pollen germination experiment and seed setting statistics found that the decrease of pollen viability of Gmarfa1a mutant resulted in the significant inhibition of seed setting Collectively， this study identified the GmARFA1a gene and uncovered its function on male fertility. It will not only enhance our understanding of the GmARFA1a and ARF gene families but also lay the foundation for further study the function of GmARFA1a genes and the utilization of heterosis in soybean.