The proliferation of barren has been reported in the coast of South Korea during decades. Algae-predator is a biological factors for barren. This study analyzed the microbiota in pharynx and gut of sea urchin, which is a major algae-predator, in urchin barren regions. Sea urchins (Mesocentrotus nudus) were collected from 5 mild- and 3 severe-barren regions. Microbiota in sea urchin and their habitat samples (sand and seawater) were analyzed using Illumina MiSeq system. The microbiota and their predicted functions were significantly different between pharynx and gut as well as between sea urchin and habitat. The microbiota in sea urchins was different according to regions, and this was related to seawater temperature, which caused differences of algae composition in each region. The differences of microbiota between mild- and severe-barren regions were analyzed by random forest model. The significantly different genera between mild- and severe-barren regions were 14 and different pathways were 11 in the pharynx, and 12 genera and 11 pathways were different in the gut. In conclusion, the microbiota in pharynx and gut was different, and the difference of microbiota between mild and severe barren regions was detected. The different microbiota between mild and severe barren regions could be due to the limited feeding algae in severe regions.