Market fresh makgeolli was stored at different temperatures of $4^{circ}C$ and $25^{circ}C$ to assess the change of the microbial diversity according to the storage temperature and period. Yeast counts increased until day 3 of storage and decreased thereafter. General and lactic acid bacterial counts continuously increased during storage. The data indicated that the control of growth of microorganisms, particularly general bacteria and lactic acid bacteria (LAB), is essential. Total acid levels started to decrease in the makgeolli stored at $4^{circ}C$, and increased from day 6 of storage in the makgeolli stored at $25^{circ}C$. The increase of total acid in the non-refrigerated condition greatly affected the quality of makgeolli. In both the fresh makgeolli samples stored at $4^{circ}C$ and $25^{circ}C$, yeast (Saccharomyces cerevisiae) and molds (Aspergillus tubingensis, Candida glaebosa, and Aspergillus niger) were noted. Denaturing gradient gel electrophoresis (DGGE) band patterns were almost constant regardless of the storage period. As for bacteria, Lactobacillus crustorum, L. brevis, and Microlaena stipoides were found in the makgeolli stored at $4^{circ}C$, and L. crustorum, Lactobacillus sp., L. plantarum, L. brevis, L. rhamnosus, and L. similis were found in the makgeolli stored at $25^{circ}C$. In particular, in the makgeolli stored at $25^{circ}C$, L. crustorum and L. plantarum presented dark bands and were identified as the primary microorganisms that affected spoilage of fresh makgeolli.