The present study was carried out to examine the distribution of six periodontopathic bacteria in deep periodontal pockets and to reconfirm the effect of Periocline on these periodontopathic bacteria. Samples from sixty-two periodontal pockets were collected at pocket depths of over 4 mm in twenty-one periodontitis patients aged 43 to 75 years. After sampling, Periocline was applied topically to the selected pockets once a week for four weeks and reexamined. The detected rates of the periodontopathic bacteria were Capnocytophaga sputigena (37.1%), Prevotella intermedia (22.6%), Porphyromonas gingivalis (22.6%), Fusobacterium nucleatum (20.1%), Actinobacillus actinomycetemcomitans (9.7%) and Eikenella corrodens (4.8%). The distribution of the bacteria was compound because two or three bacterial species were found to coexist. In view of the MIC of minocycline-HCI for these bacteria, increase of most of the measured bacteria was suppressed by the concentration of drugs, including Periocline. However, clinical strains of P. i. were considered to have low susceptibility to minocycline-HCl. In view of the effect of topical application of drugs, no significant differences were found. From these results, it was suggested that Periocline contained effective concentration of minocycline-HCl.