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Little is known about the scalp bacterial composition of alopecia areata (AA) patients. The aim of this study was to investigate the differences in the scalp microbiome of AA patients according to their prognosis, in addition to healthy controls. A total of 33 AA patients and 12 healthy controls (HC) were included in this study. The microbiomes were characterized by sequencing 16S rRNA genes on the Illumina MiSeq platform. The scalp microbiome was more diverse in AA patients compared to HC, but not significantly different according to the severity of AA. Nevertheless, the higher proportion of <i>Corynebacterium</i> species and the lower proportion of <i>Staphylococcus caprae</i> among the <i>Staphylococcus</i> species were noticed in severe AA patients compared to HC or mild AA. The higher ratio of <i>Cutibacterium</i> species to <i>S. caprae</i> was noticed in severe AA. We highlight the potential predictive role of scalp microbiome profiling to a worse prognosis of patients with alopecia areata.