Abstract: The bacterial community and diversity in the layer whole gastrointestinal tract were studied by using 16S rDNA-based denaturing gradient gel electrophoresis (DGGE) and some common and special bands were identified, in order to investigate the effect of compartment and age on the predominant eubacteria in the crop, duodenal, jejunal, ileal and ceacal digesta at the age of 2, 4, 6 and 8 weeks. The DGGE profiles provided a snapshot of the bacterial population and allowed calculation of the degree of similarity in the predominant intestinal microflora of commercial layers. PCRDGGE DNA profiles of the V3 region gene of 16S rDNA of microbiota in crop, duodenal, jejunal, ileal and ceacal digesta showed different profiles, the highest levels of diversity were found in cecum, followed by ileum and jejunum, while lowest levels of diversity were found in crop and duodenum. Similarity coefficients between banding patterns of duodenum and the other compartments were significantly different, followed by that of cecum. The number of bands in all intestinal compartants increased when layers grew from 2 to 4 weeks, then decreased in 6 weeks and increased in 8 weeks. 4 common and 9 special 16S rDNA amplicons in the DGGE pattern of layers at 8 weeks were identified by cloning and sequence analysis. Lactobacillus suntoryeus, Clostridium sordellii and E. coli were predominant in the upper GI tract. The special bacterial in ceacal digesta of commercial layers were Clostridium spp，Megamonas hypermegale and plenty of uncultured bacterial. The results of this study indicated that compartmentspecific factors play an important role in the composition and diversity of the dominant eubacterial population in every region of gastrointestinal tract of layers at different age. Furthermore the age of layers also plays an important role in the diversity of the intestinal bacterial community.