BackgroundObservational studies have shown an association between skin microbiota and alopecia areata (AA), but the causal connection remains ambiguous.MethodsWe obtained data on skin microbiota and AA from summary statistics of Genome‐Wide Association Studies and applied statistical methods from Mendelian randomization (MR) to assess causal relationships. Additionally, we investigated whether the skin microbiota acts as a mediator in the pathway from gut microbiota to AA.ResultsIn the MR analysis of KORA FF4 and AA, the inverse‐variance weighting method indicated that Corynebacterium (odds ratio [OR] = 0.82, 95% confidence interval [CI]: 0.70–0.96, p = 0.02) and asv037 (OR = 0.87, 95% CI: 0.76–0.99, p = 0.05) exerted protective effects, while Betaproteobacteria (OR = 1.21, 95% CI: 1.01–1.44, p = 0.03), asv015 (OR = 1.27, 95% CI: 1.05–1.54, p = 0.02), and Burkholderiales (OR = 1.20, 95% CI: 1.04–1.38, p = 0.01) were identified as risk factors in AA. In the MR analysis of PopGen and AA, asv001 (OR = 1.12, 95% CI: 1.01–1.24, p = 0.04), asv054 (OR = 1.13, 95% CI: 1.01–1.25, p = 0.03), and asv059 (OR = 1.14, 95% CI: 1.02–1.27, p = 0.02) were found to potentially increase the risk in AA. Furthermore, in the influence of gut microbiota on AA, the skin microbiota did not act as a mediator.ConclusionOur analysis suggests potential causal relationships between certain skin microbiota and AA, revealing insights into its pathogenesis and potential intervention strategies.