Fixed orthodontic appliances hinder the maintenance of proper oral hygiene and result in dental plaque accumulation. Many studies report that qualitative changes in the dental flora occur after initiating the orthodontic treatment, but there is a paucity of literature on the same topic among Moroccan orthodontic patients. The aim of this study was to evaluate the changes of the oral microbial flora during the orthodontic treatment period of a young Moroccan population. Materials and Methods. Dental plaque samples of 18 patients, who were randomly selected before the placement of orthodontic appliances, were collected to isolate and identify the bacterial species involved using classical bacteriological methods for species' culture and identification. The reading was recorded at T0 before placement of the device. New samples were taken again one month later and then three months afterwards, where the readings were recorded as T1 and T2, respectively. The culture was made via Columbia Agar with 5% sheep blood, Todd Hewitt Broth, and Schaedler medium containing vitamin K3. Bacterial species were identified using API-20 Strep for Streptococci and API-20 A for anaerobic bacteria. The phoenix system was used for identification. Results. After three months of orthodontic treatment, the increase in the frequency of Streptococcus sobrinus and Streptococcus mitis were significant (0.01 and 0.02, respectively) as well as for Lactobacillus (0.03). No significant difference was recorded for other bacterial species. Conclusion. There is a significant qualitative change in oral microorganisms after three months of orthodontic treatment, especially for bacteria that are incriminated in caries formation.