INTRODUCTION: Mounting evidence implicates gut microbiota in PD pathogenesis, with emerging studies suggesting this influence may be mediated by plasma metabolites. However, the causal relationships between gut microbiota and PD phenotypes (PDs), as well as whether plasma metabolites act as mediators, remain unclear. METHODS: Genetic instruments for gut microbiota, plasma metabolites, and PDs were sourced from genome-wide association studies. Bidirectional two-sample Mendelian randomization and two-step mediation analyses were performed, with False Discovery Rate (FDR) correction applied to primary analyses. Robustness was ensured through sensitivity analyses. RESULTS: After FDR correction, genus Sellimonas was identified as a robust protective factor for PD (OR = 0.784, 95% CI: 0.703 - 0.873; FDR = 0.002), while methylsuccinate was a robust risk metabolite (OR = 1.197, 95% CI: 1.118 - 1.282; FDR < 0.001). Exploratory mediation analyses identified one nominally significant protective pathway (Bacillales-methylsuccinate-PD, 12.5% mediation, p = 0.037) and one non-significant risk pathway (Senegalimassilia-S‑adenosylhomocysteine-PD, 9.7% mediation, p = 0.113). DISCUSSION: Our study provides genetic evidence for the causal associations between gut microbiota, plasma metabolites, and PDs. The most robust findings were a protective role of Sellimonas and a risk effect of methylsuccinate in PD. The exploratory pathways offer testable hypotheses for how the gut-brain axis may operate in PD pathogenesis. CONCLUSION: These findings highlight Sellimonas and methylsuccinate as targets warranting further mechanistic investigation of the gut‑brain axis in PD.