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Soybean is an important, high protein source of food and feed. However, like other agricultural grains, soybean may pose a risk to human and animal health due to contamination of the grains with toxigenic Fusaria and associated mycotoxins. In this study, we investigated the diversity of Fusaria on a panel of 104 field isolates obtained from soybean grains during the growing seasons in 2017–2020. The results of species-specific PCR analyses showed that <i>Fusarium avenaceum</i> was the most common (<i>n</i> = 40) species associated with soybean grains in Poland, followed by <i>F. equiseti</i> (<i>n</i> = 22) and <i>F. sporotrichioides</i> (11 isolates). A set of isolates, which was not determined based on PCR analyses, was whole genome sequenced. Multiple sequence analyses using <i>tef-1α</i>, <i>top1</i>, <i>rpb1</i>, <i>rpb2</i>, <i>tub2, pgk, cam</i> and <i>lsu</i> genes showed that most of them belonged to Equiseti clade. Three cryptic species from this clade: <i>F. clavum, F. flagelliforme</i> and FIESC 31 (lacking Latin binomial) were found on soybean for the first time. This is the first report demonstrating the prevalence of Fusaria on soybean grains in Poland.