The purpose of the present investigation was to study the effect of an altered subgingival environment, induced by changing the local soft tissue morphology, i.e., pocket depth reduction, on the subgingival microbiota and the clinical conditions. 7 patients aged 30-60 years with generalized marginal periodontitis were selected. Patients were instructed in proper oral hygiene and all teeth were cleaned supragingivally. Mucoperiosteal flaps were raised and the bone re-contoured to eliminate angular bony defects. While the control teeth were carefully debrided and thoroughly root planed, no root instrumentation was performed on the test teeth. Calculus deposits visible to the naked eye were only chipped-off with the tip of a scaler. The flaps were apically repositioned and sutured at the level of the bone crest. Clinical parameters showed a similar pattern of response in the test and control sites over a one year observation period post therapy. Probing depths and probing attachment levels were significantly reduced one month after surgery and remained at a lower level. A significant decrease was also noted for total anaerobic viable bacterial counts. The proportion of the Gram-negative anaerobic rods decreased significantly in both groups. P. gingivalis, Fusobacterium sp., C rectus were detected significantly less often after treatment in both groups. Capnocytophaga and A. odontolyticus, on the other hand, were more frequently isolated after therapy. These findings corroborate the concept that the reduction of selected subgingival microorganisms is the key element for the success of periodontal therapy, rather than the removal of tooth substance and mineralized deposits by root instrumentation.