Egypt is endemic with Lumpy Skin Disease (LSD) and Foot and Mouth Disease (FMD), both impose a drastic effect on the economy. These viral diseases are often complicated with secondary bacterial infections; however, scarce data is available. In this study, utilizing microbiological and molecular procedures, we identified a number of secondary bacterial infections complicating FMD- and LSD-infected cases. Moreover, the antimicrobial resistance profile of the bacterial isolates was explored. The data showed that several bacterial pathogens including Serratia odorifera, Enterococcus faecium, Paenibacillus apiaries and Microbacterium hominis could be recovered from LSD-infected cases. On the other hand, FMD cases were found to be complicated with Pseudomonas mosselii, Bacillus cereus and Trueperella pyogens. However, Bacillus licheniformis was isolated from both disease conditions. The antimicrobial testing revealed that all pathogens are resistant to more than three antibiotics of different families, indicating the multi-drug resistant capabilities of these isolates. This baseline investigation confirms the presence of many secondary bacterial infections linked to LSD and FMD as well as the widespread antimicrobial resistance among the isolated pathogens, however, the contribution of these pathogens to the mortality rate in both conditions needs further studies.