Introduction: The aim of the study was to evaluate and compare the anaerobic microflora (obligate and facultative) of the root canals of non vital teeth with periapical lesions, in diabetic (Type II) and non-diabetic patients. Methods: Access cavity preparation and collection of necrotic pulp tissue samples was done aseptically with the help of absorbent paper points placed in the canal for 60 seconds. Samples were processed anaerobically and were subjected to microbiological analysis using culture techniques for the evaluation of microbial flora. Results: There was a statistically significant difference between mean and SD values of obligate and facultative anaerobes in diabetic (Type II) and non-diabetic groups when all parameters are compared (p__ampersandsignlt;0.0001) using one-way ANOVA. Comparison of groups was done by applying Student__ampersandsignrsquo;s Unpaired __ampersandsignlsquo;t__ampersandsignrsquo; test. Obligate anaerobes were significantly more associated with cases of Type II diabetes mellitus, suggesting a role of these microorganisms in modulating the inflammatory and immunologic responses as well as its level in root canal infections which can have an influence on the pain threshold of patient. Conclusion: There were significant differences in the values of microorganisms found in Diabetic (Type II) and non diabetic patients