Background: Among the various bacterial pathogens P. multocida and R. anatipestifer cause varying degrees of mortality and morbidity leading to huge economic losses among the duck farming community. Considering the lack of information regarding the characterization of P. multocida and R. anatipestifer, a study was undertaken to establish the prevalence of these diseases in ducks from different parts of Assam, together with the capsular and virulence-associated gene characterization and antimicrobial resistance. Methods: A total of 235 samples comprising lungs, tracheal swabs, livers, heart blood and spleens collected from 47 diseased ducks, were screened for P. multocida and R. anatipestifer. The capsular and virulence-associated genes were amplified in isolated strains. The resistance pattern towards commonly used antimicrobial agents was studied by the disc diffusion method. Result: The prevalence of duck septicemia and new duck disease was confirmed in ducks of Assam, India. Molecular tools were found to be highly specific besides phenotypic-based approaches in the detection, confirmation and differentiation of both bacteria due to phenotypic similarity. The antibiotic resistance patterns of both bacteria revealed a varying degree of sensitivity toward different antibiotics.