Purpose The aim of this study was to evaluate the antimicrobial effect of photodynamic therapy (PDT) on biofilm attached to sandblasted and acid-etched (SLA) surfaces. Methods The bacterial strains used were Aggregatibacter actinomycetemcomitans and Streptococcus sanguinis. SLA disks were subdivided into five groups including one control group and four test groups (laser-alone, methylene blue (MB)-alone, PDT60, and PDT120) for PDT examination for each surface. The laser-alone group was only irradiated with a diode laser for 60 s. The MB-alone group was put into 1 ml of 100 μg/ml of methylene blue for 60 s. PDT60 and PDT120 groups were put into 1 ml of 100 μg/ml methylene blue and then irradiated for 60 and 120 s, respectively. After treatment, the survival rate of bacteria was determined by counting the colony-forming units (CFUs) after incubation. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) were used to observe the microorganisms on the disk surfaces. Results Significant differences were found between the control group, LED-alone group, MB-alone group, and PDT60 and PDT120 groups (P < 0.05). The PDT60 and PDT120 groups showed a decreasing tendency of live bacteria. In the SEM images, the control group, LED-alone group, and MBalone group showed intact bacterial cell walls. However, the bacterial cell walls were changed after PDT. On CLSM images, the PDT60 and PDT120 groups showed a high proportion of dead bacteria with red color. Conclusions These findings suggest that combination of methylene blue and a red color LED (Periowave®) was effective in reducing the viability of biofilm attached to SLA titanium surface in vitro.