To identify and characterize the microbial communities in gochujang, a traditional Korean fermented food, the viable cell numbers of total bacteria, halophilic bacteria, fungi, yeasts, halophilic yeasts, and lactic acid bacteria from 7 homemade gochujang samples produced in the Sunchang area and 5 commercial gochujang samples were counted. The variety of microflora in the gochujang samples was evaluated by identifying the isolates via DNA sequence analysis. The viable cell numbers of total bacteria were determined to be in the range of 6–7 log CFU/g, which were higher than those of yeasts. Neither lactic acid bacteria nor fungi were detected in either type of gochujang after aging. A total of 7 genera and 31 species of microorganisms were identified in the gochujang: 29% was identified as Bacillus velezensis, as a major microorganism in gochujang. Under halophilic conditions, Oceanobacillus spp. was detected for the first time.