Selenium (Se), is an essential trace element in the diet of fish and aquatic animals needed for growth, thyroid hormone metabolism, antioxidant activity, and immunity. Thus, this study has evaluated the dietary selenium yeast (Se-yeast) impact on the growth performance, antioxidant capacity, and gut bacterial community of zebrafish, Danio rerio. The fish with an average weight of 0.247 g ± 0.005 were distributed in 12 glass aquariums. 30 fish per aquarium in three replicates per group were exposed to different dietary Se-yeast concentrations: 0.3 mg/kg (control), 0 mg/kg, 3 mg/kg, and 30 mg/kg for three weeks. The result indicated a higher body weight gain and specific growth rate in the 3 mg/kg group in all groups. Se significantly accumulated in the liver, muscle, gill, and gut. The antioxidant genes superoxide dismutase 1 (SOD1), catalase (CAT), and glutathione peroxidase 1 (GPx1), and the gut marker genes: solute carrier family 15 member 1b (slc15a1b), fatty acid binding protein 2 (fabp2), cytochrome P450 family 8 subfamily B member 1 (cyp8b1), and cytochrome P450 family 3 subfamily A, polypeptide 65 (cyp3a65) were significantly expressed in the gut tissue. The 16 s rRNA sequencing showed a significant difference at phyla Proteobacteria, Fusobacteria, Firmicutes, and Actinobacteria and Cetobacterium, Aeromonas, mycobacterium, and Lactobacillus at the genus level. It was concluded that dietary Se 3 mg/kg can promote growth performance and antioxidant status, furthermore, dietary Se yeast has a significant impact on the gut microbiota of D. rerio.