Parkinson’s disease is one of the leading neurodegenerative diseases that affect elderly people around the globe. In recent years, Parkinson’s disease has been connected to gut microbiome and associations have been made among several novel species of bacteria and the development and severity of Parkinson’s disease. The aim of this study was to identify general characteristics of the gut microbiome among incident Parkinson’s disease cases and controls and by this broaden our current understanding of the topic. Statistical analyses were performed in a FINRISK 2002 population-based cohort of over 7000 people, out of which 105 incident Parkinson’s disease cases were identified and further analysed. 𝛼-diversities among the case/control groups did not differ significantly, but there seemed to be gender-based differences in the 𝛽-dissimilarity matrix between Parkinson’s disease cases and healthy controls. Additionally, a total of ten bacterial species were associated with Parkinson’s disease by the generalized linear model with nominal p-values <0.05, including for example E. hallii, C. comes, A. muciniphila, E. eligens and P. bivia. In conclusion, the gender-based variations in 𝛽-diversities and results from the regression analysis suggests that the gut microbiome may in fact be associated with the development of Parkinson’s disease.