The effects of supplementing different dietary selenium (Se) sources on intestinal histomorphology, caecal bacterial proliferation, and caecum short-chain fatty acid in layer chickens were studied. A total of 120 of 54-week-old Lohman Brown Classic laying hens were subjected to four dietary treatments: control group with no Se supplementation (T1), 0.3 mg/kg of sodium selenite (T2), 0.3 mg/kg of selenium yeast (T3), and 0.3 mg/kg of bacterial Se (Stenotrophomonas maltophilia, ADS18) (T4). All treatments were also supplemented with 250 mg/kg of vitamin E. Results showed significantly (p < 0.05) higher villus height in different small intestine parts in hens fed with diets containing organic Se sources (T3 and T4), as compared to inorganic sources (T2) and control (T1). A greater crypt depth was observed for the T1 group, as compared to T3 and T4 groups. The total bacterial populations of Bifidobacteria spp. and Lactobacilli spp. were significantly increased (p < 0.05), and tEscherichia coli population was significantly decreased (p < 0.05) in T3 and T4 groups. No effect on the total caecal short-chain fatty acid (SCFAs) content was observed. However, there was a significant increase (21.5%) of the butyric acid content in T4 group. In conclusion, organic Se supplementation, particularly bacterial organic Se, enhances intestinal histomorphology, increases the beneficial caecal bacterial proliferation, and increases butyric acid content.