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Background: The objective of this is preclinical investigation was to evaluate the differential drug sustainability and pharmacodynamic properties of two local minocycline microsphere carriers: chitosan-coated alginate (CA) and poly(meth)acrylate-glycerin (PG). Methods: Four dental implants were placed unilaterally in the edentulous mandible of six beagle dogs. Each implant was randomly assigned to receive one of the following four treatments: (i) CA (CA-based minocycline), (ii) placebo (CA substrate without minocycline), (iii) PG (PG-based minocycline) and (iv) control (mechanical debridement only). After inducing peri-implant mucositis, the randomly assigned treatments were administered into the gingival sulcus twice at a 4-week interval using a plastic-tipped syringe. Drug sustainability and pharmacodynamic (clinical, radiographical and cell marker intensity) evaluations were performed after each administration. Results: The CA microspheres remained longer around the healing abutment compared to the PG microspheres at both administrations and a longer bacteriostatic effect was observed from CA (7.0 &plusmn, 5.7 days) compared to PG (1.2 &plusmn, 2.6 days). The efficacy of the applied therapies based on clinical, radiographical and histological analyses were comparable across all treatment groups. Conclusions: CA microspheres showed longer carrier and bacteriostatic effect sustainability when compared to PG microspheres, however, longer drug sustainability did not lead to improved treatment outcomes.