Abstract Selenium (Se) is a micro-essential mineral, following the amount of Se can be appeared as selenosis or deficiency disease. Its representative role was the main compound of glutathione peroxidase as known antioxidant enzyme. This role closely relates to health of piglets. Popular form of Se was divided into organic Se (Ose) and inorganic Se (Ise) forms. Ose has greater bioavailability and costs and reduced toxicity than Ise. Mixed Se sources can save costs and improve bioavailability compared with single-source Se. This study was conducted to investigate the effects of dietary mixed Se supplementation on immune responses, stress parameter and gut microbiota of weaned pigs. Weaned pigs [n = 156; 7.85 ± 0.10 kg of initial body weight (BW)] were allotted to three dietary treatments (4 pigs/pen; 13 replicates/treatment) in a randomized complete block design (block: initial BW and sex) for 6 weeks. Dietary treatments were a corn-soybean based diet except for Se (CON), CON + 0.15 ppm Ose + 0.15 ppm Ise (A), and CON + 0.25 ppm Ose + 0.25 ppm Ise (B). On day 7, 14, and 42, blood samples were collected from randomly selected 6 pigs per treatment. The collected samples were used for immune responses and stress parameters like tumor necrosis factor-alpha, transforming growth factor beta1, interleukin-1beta, interleukin-6, and cortisol by using ELISA kits. On day 42, samples were collected to analyze microbial communities of pigs by 16s rRNA sequencing method. Microbial communities were analyzed using QIIME. The microbial alpha diversity indices such as number of OTUs, Chao1, Shannon, and Inverse Simpson were calculated to measure the within-sample diversity and richness at the species level. The microbial beta diversity was performed to inter-sample dissimilarities using weighted UniFrac distances based on principal coordinate analysis. Data were analyzed using PROC MIXED procedure of SAS. The experimental unit was a pen. The statistical model for immune responses, stress parameters and gut microbiota included dietary treatment as main effect and initial BW as a covariate. No differences were found on immune responses and stress parameters among dietary treatments. The number of OTUs, Chao1, Shannon, and Inverse Simpson were not different among dietary treatments. The Se increased (P < 0.05) relative abundance of phylum Bacteroidetes but decreased (P < 0.05) phylum Firmicutes. In addition, the Se increased (P < 0.05) relative abundance of genus Barnesiella but decreased (P < 0.05) genus Lactobacillus. In conclusion, addition of 0.3 and 0.5 ppm mixed Se can alter gut microbiota.