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Quinoa panicle rot (QPR) is a novel disease that poses a significant threat to quinoa production in China. Typical symptoms on panicles include a film of pale pink, grey‐white, or dark brown mould on the grains during the grain‐filling stage. Furthermore, QPR causes quinoa grain discolouration, unfilling, and malformation. In total, 37 isolates were identified as belonging to three species: Trichothecium roseum (nine isolates), Alternaria alternata (12), and Fusarium citri (16) based on morphology, and phylogenetic and pathogenicity characterization. The present study shows for the first time that T. roseum, A. alternata, and F. citri are the pathogens responsible for QPR. An evaluation of the growth and germination rates revealed a significant difference among the three species, with T. roseum and F. citri isolates having higher fitness in warmer (25–30℃) and humid conditions (water activity ≥0.98). However, A. alternata preferred cooler (20–25℃) and more arid conditions, and germinated in a wide range of water activities (water activity of 0.90–1.00). Among the three species, T. roseum and F. citri are probably responsible for the pink and grey diseased grains in humid regions, and A. alternata for the black‐brown diseased grains in arid regions. Pathogenicity tests showed that all three species could infect the quinoa panicles. The results of this study provide a basis for the recognition and management of QPR. [ABSTRACT FROM AUTHOR]