Cotton has a production value of US$ 45.86 million in New Mexico (USDA-NASS 2018). In June 2019, 1-2% cotton seedlings with chlorotic, necrotic or wilted leaves, or root rot were observed in six Pima cotton fields in south Las Cruces, New Mexico. Roots from five symptomatic plants sampled in each field were washed free of the soil, surface-sterilized with 0.8% sodium hypochlorite, rinsed 2-3 times with sterile distilled water, and blotted dry with a paper towel. The sterilized tissues were then dissected and plated on acidified potato dextrose agar (PDA) and incubated for 5 days at 25℃ with a 12 h dark/light photoperiod. Fungal colonies that had similar morphology were consistently isolated at 70% isolation frequency. One representative isolate from each field was selected for the following analysis. Colonies were initially white and turned pinkish 5 days later on PDA. Dark orange pigments on the bottom of plates were observed after 7 days. On PDA, the macroconidia were slender, almost straight, 3-5 septa, and medium length with a size of 25.5-41.0 × 2.8-4.5 μm (n=30). The microconidia were abundant, 0-1 septa, and oval shaped, with a size of 5.5-11.0 × 2.0-3.2 μm (n=30). Sporodochia and chlamydospores were not observed. The pathogen was therefore identified as Fusarium fujikuroi (Leslie and Summerell 2006). Genomic DNA from the isolates was extracted, and a portion of the translation elongation factor EF-1α gene (GenBank accession nos. MN896942 to MN896947), β-tubulin gene (MN896949 to MN896954) and phosphate permease (PHO) gene (MN896956 to MN896961) were amplified and sequenced using the paired primers EF-1A/EF1885R, BT-100F/BT1828R, and PHO48F/PHO2034R, respectively (Ortiz et al. 2017). BLASTn analysis of the three genes of all the isolates showed 100% (1640/1640 bp, 1694/1694 bp, and 1872/1872 bp) identity to the reference isolate of F. fujikuroi TX75 (MH828026, MH827999, and MH828057, respectively) and 99% (1634/1640 bp, 1691/1694 bp, and 1863/1872 bp) identity to another isolate (GA1A-1-1) of F. fujikuroi (KY293654, KY293646, and KY293662, respectively). A phylogenetic analysis based on the concatenated sequences clustered the six isolates with the F. fujikuroi reference isolates at 100% bootstrap support, confirming the identity of the isolates. Pathogenicity of the six isolates was tested on Upland genotype PHY 725 RF and Pima genotype PHY 841 RF. Fifty microliter conidial suspension (5 × 105 conidia ml-1) of each isolate was pipetted onto the soil around the base of the seedlings at the 1st true-leaf stage. The experiment was performed twice. Initial symptoms of wilting cotyledons were observed 7 days after inoculation (DAI). All the isolates were pathogenic to the two genotypes, causing wilting and yellowing of the leaves, rot of the root, and eventually death of some plants at 30 DAI, similar to the symptoms observed in the field. No symptoms were observed on the control plants inoculated with sterile distilled water. The average foliar disease severity rating was 2.9 on PHY 725 RF and 1.6 on PHY 841 RF on a scale of 0 for no symptom to 5 for plant death. F. fujikuroi was successfully reisolated from the roots of symptomatic plants and was identical to the isolates used for the pathogenicity test. F. fujikuroi has been reported to cause root rot and wilt on soybean (Pedrozo et al. 2015; Zhao et al. 2020), bakanae disease on rice (Carter et al. 2008) and a seedling disease on cotton (Colyer 1988). To our knowledge, this is the first report of F. fujikuroi causing wilt on cotton seedlings in New Mexico and the U.S.