A comparative analysis of the cultivable intestinal microbiota of farmed (AF) and wild-caught (WF) Paralichthys adspersus was performed. The 16S rRNA gene was used for taxa identification, and the ITS region for strain differentiation. We detected the presence of Vibrio, Bacillus, Photobacterium, Staphylococcus and Carnobacterium in AF, and Exiguobacterium, Klebsiella, Arthrobacter, Raoultella, Kluyvera, Myroides, Streptococcus, Vagococcus, Staphylococcus, Acinetobacter, Psychrobacter, Lactobacillus, Weissella and Lactococcus in WF. The microbial community was more diverse in WF than in AF. Some bacterial groups were only found in wild-caught fish and may be studied as potential beneficial agents for improving production traits in farmed fish. As the first study of microbiota of P. adspersus, it provides significant information that can potentially help improve farming practices by using strains as species-specific probiotics.