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Matrix metalloproteinases (MMPs) represent a family of 23 zinc-dependent endopeptidases central to extracellular matrix remodeling in periodontal and peri-implant diseases. This comprehensive review examines the pathogenic mechanisms, diagnostic applications, and therapeutic targeting potential of the entire MMP family in periodontitis and peri-implantitis. All MMP subfamilies, collagenases (MMP-1, -8, -13), gelatinases (MMP-2, -9), stromelysins (MMP-3, -10, -11), matrilysins (MMP-7, -26), membrane-type MMPs (MT1-6), and others, demonstrate distinct expression patterns and substrate specificities in diseased tissues. MMP-8 and MMP-9 emerge as primary biomarkers, showing 5-6-fold elevations in active periodontitis compared to health, with corresponding increases in activation ratios and decreases in tissue inhibitor of metalloproteinase (TIMP) levels. Diagnostic applications reveal point-of-care active MMP-8 (aMMP-8) immunotests achieve 70%-85% sensitivity and 65%-80% specificity for periodontitis detection, though standardization challenges limit clinical implementation. Salivary and gingival crevicular fluid MMP profiling demonstrates disease-specific signatures, with MMP-8/TIMP-1 ratios serving as progression indicators. Therapeutically, MMP modulation strategies include FDA-approved subantimicrobial dose doxycycline (SDD), which achieves a 40%-60% reduction in clinical attachment loss. Novel approaches encompass selective MMP inhibitors, pro-resolving mediators, and host-modulation therapies, with emerging AI-assisted personalized treatment protocols showing promise. Critically, peri-implantitis exhibits more severe MMP dysregulation than periodontitis, with MMP: TIMP ratios reaching 50:1 versus 20:1, accelerated bone loss patterns, and distinct MT-MMP involvement reflecting titanium surface interactions. Translation barriers include the need for biomarker standardization, the complexity of MMP redundancy, and the requirement for personalized diagnostic thresholds. Future directions emphasize integrating MMP signatures with multi-omics approaches, developing selective inhibitors, and establishing evidence-based clinical guidelines for MMP-targeted precision periodontal medicine.