Four rough‐surfaced (R) and three smooth‐surfaced (S) clinical isolates ofCapnocytophagaobtained from the subgingival plaque of periodontitis patients were studied for their peptidase and protease profiles. The results were compared with those obtained withC. gingivalis(which has a smooth morphology). All cell extracts obtained by ultrasonic treatment displayed high peptidase activity towardN‐aminoacyl‐2‐naphthylamines, the best substrates being the arginyl, aspartyl, and leucyl derivatives. The R and S isolates did not differ in these enzyme activities. Also the protease profiles studies with 4‐phenylazobenzyloxy‐carbonyl‐L‐prolyl‐L‐leucylglycyl‐L‐prolyl‐D‐arginine (PZ‐PLPGA) and casein were similar. All extracts also hydrolyzed furylacryloyl‐L‐leucylglycyl‐L‐prolyl‐L‐alanine (FALGPA), reconstituted type I [3H]‐collagen, and gelatin. NaBenzoyl‐DL‐arginyl‐2‐naphthylamine was hydrolyzed faster by the R than the S strains. Comparison between cell suspensions and cell extracts ofC. gingivalisshowed the suspensions to be enzymatically more active than the extracts. In general, peptidase substrates and PZ‐PLGPA were hydrolyzed at a higher rate by suspensions than by extracts, while protease substrates (such as casein) were hydrolyzed faster by the extracts. Gelatin and FALGPA were hydrolyzed by cell extracts only. Fast protein liquid chromatography of peptidases on a gel column was found to be a suitable method to differentiate between R and S isolates in diagnostics, while the chromatographic p