Fusarium wilt, a vascular wilt caused by Fusarium oxysporum, has been a serious problem for birdsfoot trefoil (Lotus corniculatus) production in parts of New York and Vermont since the 1970s, causing wilt, severe root necrosis, and rapid plant death. Analysis of F. oxysporum isolates causing this disease indicated that the pathogen has a unique host range relative to previously designated F. oxysporum formae speciales and is monophyletic. Pathogenic isolates from New York and Vermont caused severe vascular wilt of trefoil and moderate vascular wilt of pea but no disease on alfalfa, red clover, soybean, or dry bean. The host range of trefoil isolates was distinct from F. oxysporum isolates pathogenic to other legumes. F. oxysporum isolates pathogenic to trefoil belonged to a single vegetative compatibility group separate from nonpathogenic isolates and shared identical mitochondrial small subunit rDNA, translation elongation factor 1-alpha, and nuclear rDNA intergenic spacer haplotypes. Phylogenetic analysis of the concatenated sequence data assigned isolates pathogenic to trefoil to a single, well-supported clade distinct from other pathogenic F. oxysporum. We propose designating the fungus Fusarium oxysporum Schlechtendahl emend. Snyder & Hansen f. sp. loti forma specialis nova.