Fixed or removable orthodontic appliances impede the maintenance of oral hygiene and result in plaque accumulation. 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 the present study was therefore done to determine the amount microbial colonization with two different archwire ligation techniques. Twenty subjects for this study were randomly selected. Amount of microbial colonization was evaluated from both right and the left sides of the maxillary dental arch at day 1 that is (after receiving through oral prophylaxis) and then the arch wire was ligated with split mouth technique using stainless steel ligature wire and elastomeric ring. Second culture was done at day 21 (21 days after arch wire was ligated), the aerobic and anaerobic bacterial count was then compared. Paired t test showed significant difference in bacterial count with stainless steel ligature wire and elastomeric ring. The teeth ligated with elastomeric rings exhibited significantly greater number of both the aerobic and anaerobic microorganisms than the teeth ligated with steel ligatures in both the groups.