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A new emerging disease of quinoa, quinoa basal stem rot (QBSR), has been recorded in Shanxi Province, China. Observed during the inflorescence emergence stage, the pathogen causes wilting, foliar chlorosis, leaf abscission and eventual death of quinoa. In this study, isolates were identified as Fusarium solani using morphology, molecular and phylogenetic analysis (using sequences of calmodulin, rDNA internal transcribed spacer region, RNA polymerase II B‐subunits RPB1 RPB1 and RPB2 RPB2, and translation elongation factor 1‐α), and pathogenicity analysis. Twenty‐seven isolates were classified into two different groups according to their morphological characteristics, and the mycelial growth rate of Group 2 was higher than that of Group 1 on six different media. The optimum growth temperature for both groups was 30°C and the highest mycelial growth rates were 9.2 and 10.0 mm/day, for Groups 1 and 2, respectively. The sporodochial conidia (SC) and aerial conidia (AC) germinated normally at 15–25°C and 10–40°C, respectively, and the width of SC and AC germ tubes were 1.4 and 2.2 μm. The lethal temperature for AC was 51°C for 20 min, and SC stopped germinating at 45°C. Pathogenicity tests of representative isolates showed that mycelia or conidia caused typical symptoms of QBSR on wounded basal stems of Chenopodium quinoa at 6 days postinoculation. The optimum temperature for the onset of QBSR was 30°C for both groups of isolates, and lesion lengths ranged from 5.4 to 5.9 cm. Knowledge of this pathogen will provide useful information for effective disease management to prevent its spread. [ABSTRACT FROM AUTHOR]