Objective To evaluate the effects of different dental filling materials in wedge-shaped defect restorations on microbial colonization in supragingival plaque and gingival crevicular fluid. Methods Fifty-seven patients with wedge-shaped defect of maxilla first premolars were selected, and were randomly filled with resin-modified glass ionomer (RMGI group, n=19), polyacid-modified composite resin (PMCR group, n=20) and composite resin (CR group, n=18) for restorations. The numbers of colonies of Streptococci mutans and Actinomyces viscosus in supragingival plaque and anaerobic Gram-positive （G＋）rod bacillus and anaerobic Gram-nagative （G－）rod bacillus in gingival crevicular fluid were recorded before restorations and 3 months and 6 months after restorations, respectively. The contralateral corresponding teeth were served as controls. Results There was no significant difference in the numbers of colonies among RMGI group, PMCR group, CR group and control groups before restorations (P>0.05). The number of colony of Actinomyces viscosus in supragingival plaque in RMGI group and that of anaerobic G＋ rod bacillus in gingival crevicular fluid in CR group were significantly larger than those in control groups 3 months and 6 months after restorations （P<0.05）. Conclusion RMGI and CR for wedge-shaped defect restorations may have adverse effects on microbial colonization in supragingival plaque and gingival crevicular fluid, while PMCR has advantages in anti-caries and reducing periodontal tissue injury in wedge-shaped defect restorations.