This study was to observe and compare the microbiological effects of laser therapy combined with ultrasonic subgingival scaling and root planning (SRP) versus SRP alone.26 contra lateral teeth were randomly assigned to the test group (laser + SRP) or the control group (SRP alone). Subgingival microbial samples were collected, cultured and analyzed at baseline, then repeated immediately after laser treatment at week 1, week 2 and week 4.Although both groups had significant increase in G+/G- ratio (P < 0.01), the changes of G+ and G- were more obvious in the test group till week 1(P < 0.05). The total CFU of test group diminished significantly just after laser irradiation (P < 0.05). That revealed the laser therapy followed by SRP appeared to have a stronger effect on converting the subgingival micro-ecosystem to healthy status.Laser appeared to have a stronger bactericidal action in vivo. especially on the dark-pigmented G- rods associated with periodontal disease.