Preeclampsia is a severe pregnancy-related inflammatory disease without an effective treatment. The pathophysiology remains partly unknown. However, an increased inflammatory response and oxidative stress are part of the maternal systemic reaction. Recent data have suggested that dysbiosis of the gut microbiome plays a role in preeclampsia as well as other inflammatory diseases. However, dysbiosis in preeclampsia has not been studied in a Scandinavian population. Furthermore, although the fungal flora may also have anti-inflammatory properties, it has never been studied in preeclampsia. We included 25 preeclamptic and 29 healthy third-trimester women for the ITS and 16S sequencing of fungal and bacterial microbiota, respectively. Calprotectin was measured to assess systemic and intestinal inflammatory responses. The fungal diversity differed with BMI and gestational length, suggesting a link between fungi and the immune changes seen in pregnancy. An LEfSe analysis showed 18 significantly differentially abundant bacterial taxa in PE, including enriched Bacteroidetes and depleted Verrucomicrobia and Syntergistota at the phylum level and depleted Akkermansia at the genus level, suggesting a role in the pathophysiology of PE.