Three types of nuruk were made from rice, wheat, and a rice-glasswort (6:4) mixture. Nuruk, makgeolli, and vinegar were manufactured with rice nuruk (RN), wheat nuruk (WN), and rice-glasswort nuruk (RGN). The saccharifying activity and ethanol productivity of nuruk, polyphenol content in makgeolli, and acetic acid and polyphenol content in the vinegar were increased as the result of the addition of glasswort. The variable region of 18S- or 16S-rDNA amplified with genomic DNA extracted directly from nuruk, makgeolli- and vinegar-making cultures was analyzed via temperature gradient gel electrophoresis (TGGE). The sequence of the 18S-rDNA variable region extracted from the TGGE gel for nuruk was more than 95% homologous with Aspergillus sp and that for the makgeolli-making culture was more than 95% homologous with Saccharomyces sp and Saccharomycodes sp. The sequence of the 16S-rDNA variable region extracted from TGGE gel for the vinegar-making culture was more than 95% homologous, primarily with the Acetobacter sp. The eukaryotic and prokaryotic diversity in the nuruk, makgeolli-making, and vinegar-making cultures was not significantly altered by the addition of glasswort. Prokaryotic diversity was higher than eukaryotic diversity in the nuruk, but eukaryotic diversity was higher than prokaryotic diversity in the makgeolli-making culture, on the basis of the TGGE patterns. No 18S-rDNA was amplified from the DNA extracted from the vinegar-making culture. In conclusion, the glasswort may be not simply an activator for the growth of microorganisms during the fermentation of nuruk, makgeolli, or vinegar, but also a nutritional supplement that improves the quality of vinegar.