Objective To investigate the changes of subgingival bacterial communities in periodontal pockets with different depth using denaturing gradient gel electrophoresis (DGGE) analysis. Methods Two patients with chronic periodontitis (patient 1 and patient 2) were selected, and subgingival plaque samples of the same sampling sites were obtained from two patients before basic periodontal treatment and 6 weeks, 12 weeks, 18 weeks and 12 months after mechanical debridement. Total microbial genomic DNA of the plaque samples was extracted, and V3-V5 region of 16S rDNA of all bacteria was amplified by PCR and separated by DGGE. Total numbers of bands and similarity coefficients were calculated, and clustering patterns of samples from individuals were analysed. Results After mechanical debridement, the probing depth decreased in both patients with different levels (≤3 mm in patient 1 and ≥5 mm in patient 2). After treatment, there was no significant change in numbers of bands in DGGE analysis in both patients, with similarity coefficients of 48.14%-57.8% and 63.70%-72.35% respectively compared with the baseline. Furthermore, cluster analysis indicated significant changes in bacteria diversity 6 weeks after mechanical debridement, followed by gradual shift over time. Conclusion Although periodontal pockets decrease in depth, re-colonization of periodontal bacteria may occur soon after mechanical debridement in patients with chronic periodontitis.