BACKGROUND AND AIM: Peroxisome proliferator-activated receptors (PPARs), as nuclear receptors, modulate both lipid metabolism and inflammatory/immune processes. This study examines the impact of modulating the activities of the PPAR subtypes PPARbeta/eth and PPARgamma on the gut microbiota in inflammatory bowel disease (IBD). METHODS: Mice with dextran sulfate sodium (DSS)-induced acute colitis were treated with the PPARgamma agonist pioglitazone, PPARbeta/delta agonist GW0742, or their respective antagonists (GW9662, GSK3787). Weight loss, diarrhea severity, hematochezia, and disease activity index were assessed daily. Upon study completion, colon length, histopathology, and mRNA levels of the intestinal barrier and inflammatory markers were measured. Occludin and E-cadherin levels were assessed via immunofluorescence analysis, and cecal samples underwent 16S rRNA sequencing for gut microbiota analysis. RESULTS: Our findings revealed that the agonists pioglitazone and GW0742 effectively suppressed DSS-induced colitis, improved clinical symptoms, reversed colon shortening, and mitigated histological damage. Conversely, their antagonists, GW9662 and GSK3787, failed to alleviate inflammation and sometimes exacerbated disease indicators. Both agonists modulated DSS-induced dysbiosis by reducing the abundance of proinflammatory cytokine-associated microbiota, including Bacteroides, Enterococcus, and Escherichia-Shigella, while enhancing both alpha-diversity and beta-diversity of the gut microbiome, to restore equilibrium. CONCLUSION: Our findings reveal that activation of PPARgamma and PPARbeta/delta can balance the gut microbiota in mice and ameliorate experimental colitis in mice. Thus, PPARgamma and PPARbeta/delta have protective effects against IBD and could serve as novel therapeutic targets for its treatment.