This study is to investigate and characterize the microbiota composition on eggshells from 3 different areas of Shaanxi province (Yulin, Hanzhong and Xi'an). The eggs were stored at 25 degrees C for 56 days and bacterial samples were collected from eggshells on day 0, 14, 28, 42 and 56. Denaturing gradient gel electrophoresis and high-throughput sequencing of 16S rRNA hypervariable region V3-V4 were performed. Alpha diversity was applied for analyzing the diversity of samples through 6 indices, including Observed-species, Chao1, Shannon, Simpson, ACE and Good's-coverage. Beta diversity was used to study the similarities or differences in the community composition of the samples. Totally, 36 phyla and 595 genera were classified by 16S rRNA gene sequencing. The composition of the microbial communities of different regions was quite different. Firmicutes (33-38% of total phyla) and Actinobacteria (36-61% of total phyla) were the most abundant phyla in all three regions. Proteobacteria were relatively more abundant (about 18% of total phyla) on eggs from Hanzhong. During storage time, the microbial communities mainly changed from Firmicutes to Actinobacteria on eggs from Yulin and Xi'an.Lactobacillus, KocuriaandStreptomyceswere much higher at the genus level. Spoilage bacteriaStaphylococcus, Streptococcus, PseudomonasandEnterococcuswere detected at the genus level.Campylobacter jejuni(< 1% of total bacteria), which might be related to human illness, was also detected. In conclusion, the structure, abundance, and composition of microbiota on eggshells differ among areas. The microbiota changed regularly during storage time. The current study may offer a new insight into bacterial species on eggshells.