The intestinal barrier includes physical and chemical components for preventing the invasion of pathogenic and toxic agents. The aim of this study was to investigate small intestinal morphology, antimicrobial peptides, and tight junction (TJ) distribution among broilers, Thai Betong chickens, and native Thai Praduhangdum chickens. Intestinal samples from 40 chickens of each breed were collected. The results of the histological and morphological examination revealed that the duodenum of all breeds had the maximum villus height compared to the other parts. The intestinal tract of both Betong and Praduhangdum chickens was low in the number of mucin and goblet cells. In broilers, the intestinal surface mucins correlated with the number of β-defensin-positive Paneth cells. Claudin-1 protein was observed in the cytoplasm of the epithelium in all breeds, with the highest intensity of claudin-1 staining detected in the intestinal cells of the ileum. Localization of occludin was higher in the broilers in all intestinal segments than in the native Thai chickens. In conclusion, the broilers exhibited a large amount of TJ proteins and mucosal immunity as compared to native Thai-breed chickens. TJ localizations together with intestinal morphology and mucosal immunity can be utilized as biological markers for gut health.