The outer keratin layer of crocodile skin forms a physical barrier against mechanical damage and pathogens. However, if breached, the resulting damage can cause the skin to be downgraded, and even rejected, from entering the skin trade compromising industry sustainability and the sustainable-use conservation programs they support. In an ongoing attempt to improve crocodile skin quality, conventional bacterial culturing from skin lesions has not been useful for distinguishing normal from blemish-associated bacteria. Instead, we used 16S rRNA gene tag sequencing to characterise the bacterial microbiota of wild and captive blemish-free crocodile skins to identify which bacteria are associated with linear blemishes. The microbiota of wild crocodile skin differed from farmed animals with the exception of the Order Pseudomonadales which appeared to be commensal on both. Bacteria significantly associated with linear lesions belonged to the genera Clostridium and Petrimonas. Clostridia bacteria are known to produce collagenases (enzymes) which can digest collagen which warrants further investigation into potential detrimental effects on blemish healing impairment. However, the genus Dermatophilus (class Actinobacteria), with multiple sequence variants, was significantly more abundant in lesion samples compared to blemish-free skin. This genus has not been associated with linear lesions previously but has been reported to cause “brown spot” on Crocodylus porosus skins whereby filamentous hyphae infiltrate the dermal layers of the skin. This result requires further investigations including the development of a Dermatophilus-specific test to study its occurrence across farms and to manipulate water quality and hygiene regimes to reduce the environmental and skin loadings of this organism.