Recently greater attention has been given to hides and skins because of the added value of processing them into leather and leather products. The study aimed to isolate and identify aerobic bacteria associated with damage to raw cattle hides and sheep/goat skins in Sudan. Probably due to poor hygiene and poor conditions in the slaughterhouses a total of 414 organisms were isolated (379 Gram- positive and 35 Gram- negative bacteria) from fresh and washed hides and skins in the slaughterhouse, salted and dried hides and skins in warehouses where these was a delay in curing and the absence of bactericides. Other bacterial species were isolated from raw hides and skins which were delivered without treatment to the tannery. Staphylococcus spp., Micrococcus spp., Corynebacterium spp., Bacillus spp., Escherichia coli and Pseudomonas spp. were the predominant microorganisms isolated. Histological examination of the putrefied areas showed that the epidermis became thin without cellular structure and appeared ribbon-like and detached from the dermis whilst the dermis became loose. The bacterial damage was clear in raw hides and skins delivered without treatment and had lesions of putrefaction with St. equorum, St. gallinarum, Dermacoccus nishinomiyaenesis, Gardnerella vaginalis being isolated from putrefied hides and skins for the first time. Significance and impact. The bacterial activity affected skins and hides structures. The epidermis and dermis layers, which are valuable tissues in the leather industry and determine the quality of the leather were severely affected.