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Background: Peri‐implantitis and periodontitis have similar immunological bioprocesses and inflammatory phenotypes. In the inflammatory process, the adaptive immune cells can drive the development of disease. This research investigated the differences and diagnostic significance of peri‐implantitis and periodontitis in adaptive immune responses. Methods: We acquired four GEO datasets of gene expressions in surrounding tissues in healthy person, healthy implant, periodontitis, and peri‐implantitis patients. The structural characteristics and enrichment analyses of differential expression genes were examined. The adaptive immune landscapes in peri‐implantitis and periodontitis were then evaluated using single sample gene set enrichment analysis. The STRING database and Cytoscape were used to identify adaptive hub genes, and the ROC curve was used to verify them. Finally, qRT‐PCR method was used to verify the expression level of Hub gene in activated T cells on the titanium‐containing or titanium‐free culture plates. Results: At the transcriptome level, the data of healthy implant, peri‐implantitis and periodontitis were highly dissimilar. The peri‐implantitis and periodontitis both exhibited adaptive immune response. Except for the activated CD4+T cells, there was no significant difference in other adaptive immune cells between peri‐implantitis and periodontitis. In addition, correlation analysis showed that CD53, CYBB, and PLEK were significantly positively linked with activated CD4+T cells in the immune microenvironment of peri‐implantitis, making them effective biomarkers to differentiate it from periodontitis. Conclusions: Peri‐implantitis has a uniquely immunogenomic landscape that differs from periodontitis. This study provides new insights and ideas into the activated CD4+T cells and hub genes that underpin the immunological bioprocess of peri‐implantitis. [ABSTRACT FROM AUTHOR]