Prevotella intermedia and Porphyromonas gingivalis are two of the specific microorganisms that frequently occurs in chronic periodontitis. As protein plays an important role in bacteria's life and its virulence factor, we tried to explore variation in P. intermedia and P. gingivalis cell protein profile which isolated from different periodontl pocket depth of chronic periodontitis patient. P. intermedia and P. gingivalis were identified using Polymerase Chain Reaction (PCR) technique, and its protein profile were evaluated using Sodium Dodecyl Sulfate - Polyacrylamide Gel Electrophoresis (SDS-PAGE). SDS-PAGE result showed that there were significant difference between protein profile of P. intermedia cell which isolated from slhallow and deep pocket with dominant proteins of molecular weight 200 kDa, 110 kDa, 40 kDa, and 25 kDa, however, relationship between pocket depth and P. intermedia cell protein pofile could not be concluded because unrepresentative number of P. intermedia colonies. In the other hand the variation in P. gingivalis cell protein profile was not influenced by pocket depth with dominant protein called hemin binding protein (HbBp).