Objective To investigate the effects of periodontal therapy on Archaea colonization in subgingival plaque. Methods The periodontal treatment process of 49 patients with moderate to severe periodontitis were followed up, and subgingival plaque samples were collected after supragingival plaque scaling (baseline), 4 weeks after periodontal basic treatment and 12 weeks after periodontal flap surgery for DNA extraction. PCR was performed with 16S rRNA gene of Archaea, and the expression of 16S rRNA of Archaea in plaque samples was qualitatively detected. The positive samples were determined, and the detection rate of Archaea was calculated. Real-Time PCR was employed to quantitatively detect the 16S rRNA gene of total bacteria and Archaea in positive samples, and the relative abundance of Archaea was calculated. Results The detection rates of Archaea and relative abundance of Archaea in subgingival plaque samples 12 weeks after periodontal flap surgery were 17.6% and 0.58% respectively, which were significantly lower than those at baseline (69.4% and 2.32%) and 4 weeks after periodontal basic treatment (57.1% and 2.30%)（P<0.05）. Conclusion The Archaea colonization in subgingival plaque rapidly decreases with the periodontal treatment process, which indicates that the subgingival anaerobic environment is the key factor for Archaea colonization.