Septoria glycines, the causal agent of Septoria brown spot, is the most widespread foliar disease of soybean. The absence of a high-quality reference genome has hindered population genomics research and constrained the ability to investigate fungicide resistance and virulence in this pathogen. Here, we present a reference-quality, telomere-to-telomere genome assembly for S. glycines. This resource provides a foundation for comparative genomic analyses, fungicide resistance surveillance, and effector identification.