Bactericidal and detoxification effects of diode laser (DL) have been reported in periodontal treatment. The objective of this study was investigating the additional effect of DL with nonsurgical periodontal treatment on the red complex bacteria in type 2 diabetes mellitus (DM) patients with chronic periodontitis (CP). Sixty type 2 DM patients with chronic periodontitis (CP) were randomly assigned in two parallel groups to receive scaling root planning (SRP, n = 30) or SRP followed by DL periodontal pocket irradiation (SRP + DL, n = 30). Recording of clinical parameters and subgingival plaque sampling were performed at baseline, and post therapy (1 and 3 months after treatment). Amounts of Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia were evaluated with quantitative RT-PCR. Significant reductions for numbers of all three bacterial species were observed at 1 and 3 months compared with baseline for both treatments (p < 0.001), but no significant differences were found between two groups regarding bacterial reductions at these follow-up time points. No additional benefit of DL as an adjunct to nonsurgical periodontal therapy was recognized in the reduction of P. gingivalis, T. denticola, and T. forsythia for type 2 DM patients with CP. Further studies are required to clarify the effects of diode laser on the other periodontopathogens.