Abstract: Background and Objective: Mannheimia haemolytica (M. haemolytica) and Pasteurella multocida (P. multocida) are non-motile, Gram-negative coccobacilli bacteria responsible for considerable economic losses in farm animals. This study aimed to use the random amplification of polymorphic DNA (RAPD) and enterobacterial repetitive intergenic consensus (ERIC) markers for characterization and differentiation between M. haemolytica and P. multocida and whether, they can be used as diagnostic tools. Materials and Methods: Blood and lungs samples were collected from infected sheep and goats. Biochemical tests were used to identify the isolated microorganism. The extracted DNA from the positive isolates was used for the molecular characterization using RAPD and ERIC markers. Results: The biochemical tests showed 11 positive isolates of M. haemolytica and 6 positive isolates of P. multocida. The molecular characterization of M. haemolytica and P. multocida showed genetic heterogeneity between the isolates. The different RAPD markers showed different molecular patterns between M. haemolytica and P. multocida. The result of ERIC marker is characteristic for each Pasteurellaceae species. The ERIC assay patterns presented obvious differentiation between the two species. Conclusion: The RAPD markers clarified that the molecular characterization of M. haemolytica and P. multocida was genetic heterogeneity. ERIC marker is effective molecular tool for epidemiological studies and differentiation between Pasteurellaceae family (M. haemolytica and P. multocida).