Fixed or removable orthodontic appliances impede the maintenance of oral hygiene and result in plaque accumulation. Plaque retention surrounding orthodontic appliances leads to enamel demineralization caused by organic acids produced by bacteria in the dental plaque. Many studies have evaluated the effects of fixed orthodontic appliances on microbial flora and periodontal status, but only a few have evaluated the method of ligation as an additional factor. The aim of this study was to determine the changes in microbial flora and periodontal status after orthodontic bonding and to determine whether two different archwire ligation techniques affect these changes. A total of 21 orthodontic patients scheduled for fixed orthodontic treatment were selected for this split-mouth study. Two commonly used auxiliaries (elastomeric rings and ligature wires) for tying archwires were tested. Microbial and periodontal records were obtained before bonding (TO), one week later (T1), and five weeks after bonding (T2). Paired t-test and Wilcoxon signed rank test were used to compare the groups statistically. Although, teeth ligated with elastomeric rings exhibited slightly greater numbers of microorganisms than teeth ligated with steel ligature wires, the differences were not statistically significant and could be ignored. The two archwire ligation techniques showed no significant differences in the gingival index, bonded bracket plaque index, or pocket depths of the bonded teeth. However, teeth ligated with elastomeric rings were more prone to bleeding. Therefore, elastomeric ring use is not recommended in patients with poor oral hygiene.