This study investigated effects of dietary fumonisins (FBs) on gut and faecal microbiota of weaned pigs. In total, 18 7-week-old male pigs were fed either 0, 15 or 30 mg FBs (FB1+ FB2+ FB3)/kg diet for 21 days. The microbiota was analysed with amplicon sequencing of the 16S rRNA gene V3-V4 regions (Illumina MiSeq). Results showed no treatment effect (p> 0.05) on growth performance, serum reduced glutathione, glutathione peroxidase and malondialdehyde. FBs increased serum aspartate transaminase, gamma glutamyl-transferase and alkaline phosphatase activities. A 30 mg/kg FBs treatment shifted microbial population in the duodenum and ileum to lower levels (compared to control (p< 0.05)) of the familiesCampylobacteraceaeandClostridiaceae, respectively, as well as the generaAlloprevotella,CampylobacterandLachnospiraceae Incertae Sedis(duodenum),Turicibacter(jejunum), andClostridium sensu stricto 1(ileum). Faecal microbiota had higher levels of theErysipelotrichaceaeandRuminococcaceaefamilies andSolobacterium,Faecalibacterium,Anaerofilum,Ruminococcus,Subdoligranulum,Pseudobutyrivibrio,CoprococcusandRoseburiagenera in the 30 mg/kg FBs compared to control and/or to the 15 mg/kg FBs diets.Lactobacilluswas more abundant in the duodenum compared to faeces in all treatment groups (p< 0.01). Overall, the 30 mg/kg FBs diet altered the pig gut microbiota without suppressing animal growth performance.