Seahorse aquaculture has been a focus for meeting the demand of Chinese traditional medicine and aquarium, and one of the bottlenecks for aquaculture is disease. The present study focused on the intestinal microbiota between wild and cultured seahorses. Results showed that the Alcaligenaceae and Enterobacteriaceae were the dominant intestinal flora in intestinal tracts of seahorses, and Achromobacter sp., Serratia marcescens, and Serratia sp. were the dominant intestinal flora. It was the first time that two strains (TPL14 and yb97) of Achromobacter xylosoxidans were found in cultured seahorses and even in fishes. Interestingly, Vibrio, which accounted for 19.35% of the intestinal bacterial communities, only occurred in the cultured seahorses, and it was strongly involved in the intestinal diseases in seahorse H. trimaculatus.