The current study was conducted to isolate, test and characterize molecularly and physiologically lactic acid bacteria from the intestines of Muscovy ducks to evaluate their probiotic potential for poultry farming. Three hundred lactic acid bacteria from the gastrointestinal tract of Muscovy ducks were isolated. The strains were phenotypically characterized by observing cell morphology, performing Gram staining, catalase production, and testing their ability to grow in MRS broth at different temperatures, pH values, NaCl concentrations, bile concentration, and in compatibility tests between strains. Nine strains were selected based on their resilience. Eight strains were identified using molecular techniques. These strains exhibited significant tolerance to acidic pH, bile salts, and NaCl, essential for probiotic function. All isolates inhibited the growth of Salmonella enterica serotype Typhimurium (DT104) and Enteropathogenic Escherichia coli serotype O86:H34 (EPEC), showcasing their antimicrobial potential. Antibiotic susceptibility testing revealed 100% resistance to clindamycin and erythromycin but high susceptibility to ampicillin and vancomycin. Growth was observed at various temperatures, indicating mesophilic characteristics. Compatibility tests confirmed their suitability for probiotic formulations. Genomic analysis identified the strains primarily as Enterococcus. Conclusively, the study identified eight out of nine selected lactic acid bacteria strains from Muscovy ducks as autochthonous probiotics, showing resilience to treatments and compatibility for consortium formulation. These strains are suitable for in vivo testing for potential poultry farming applications. Further research on their molecular mechanisms and in vivo effects is needed.