This study endeavored to investigate the diversity of microbes present during the shaping, ripening and drying of Daqu, a fermentation starter culture and substrata complex of Maotai alcoholic spirit. A nested PCR-denaturing gradient gel electrophoresis technique was utilized with different combinations of primers. The results showed the presence of bacteria, yeasts and molds. The microflora, which originate from wheat, were readily detectable during every stage of the fermentation process. However, the microbial structure had clear differences in the shaping, ripening and drying processes. In the shaping stage, there was a high level of diversity of the LAB (lactic acid bacteria) and fungi in the shaped samples. In the ripening stage, however, a reduction of diversity of fungi with a high level of diversity of the Bacilli was observed in the ripened samples. In the drying stage, the diversity of Bacilli and fungi, especially acid-producing bacteria, reduced dramatically. Interestingly, uncultured Lactococcus sp., Microbacterium testaceum, Cochliobolus sp., and Thermoascus crustaceus were the first to be detected in the fermentation starters used in liquor production. This study revealed the microbial diversity and distributions during the shaping, ripening and drying of Daqu-making, facilitating evaluation of the hygienic conditions and aiding in the design of specific starter and/or adjunct cultures.