Abstract: Background – Gastrointestinal microbiota and metabolic by-products stimulate glucagon-like peptide-2 (GLP-2) secretion from enteroendocrine cells. GLP-2 is responsible for intestinal mucosal barrier maintenance. Chronic enteropathy (CE) in dogs is associated with decreased plasma GLP-2 concentrations and microbiome dysbiosis.Objectives - To determine the association between gastrointestinal microbiota populations and plasma GLP-2 concentrations in dogs with CE.Animals – 18 client-owned dogs with uncontrolled idiopathic CE and 16 client-owned healthy control (HC) dogs.Methods – Untargeted 16S V4 rRNA and targeted (dysbiosis index) microbiome analysis was performed on fecal samples collected prospectively from HC dogs and CE dogs prior to and 1 month after initiation of individualized CE treatment. Plasma GLP-2 was measured concurrently (ELISA). Diversity indices (Shannon diversity, principal coordinate analysis) and bacterial abundances were compared between groups and time-points. Taxa associated with differences in GLP-2 concentrations among groups were identified using principal component analysis followed by least squares regression.Results – While targeted analysis did not identify taxa associated with plasma GLP-2 (R2= 0.157; F (7,38)= 1.007; P= .442), untargeted genomic sequencing identified 6 families (R2= 0.319; F (5, 40)= 3.741; P= .007) and 19 genera (R2 =0.276; F (2,43)= 8.190; P= .001) that contributed to group variance in GLP-2 concentration.Conclusion and clinical importance – Gastrointestinal microbiome dysbiosis may contribute to decreased plasma GLP-2 concentrations in dogs with CE. Given the role of GLP-2 in maintaining normal intestinal mucosal structure, further exploration into the interrelation of dysbiosis with CE pathophysiology and treatment is warranted.