Filariasis in dogs is caused by several species of filariids. Because of importance of this infection in veterinary medicine and public health, it is necessary to carry out an epidemiological and cross sectional studies in various geographical areas and use of well-adapted diagnosis methods. In this study 205 capillary and whole blood samples were collected from doges in various counties of East-Azerbaijan province. Samples after preparation were examined by Knott`s test and light microscope for presence of microfiler. In molecular identification, Pan-filarial and species-specific PCR perimers was used to differentiate among Dirofilaria immitis, Dirofilaria repens, Acanthocheilonema reconditum, Acanthocheilonema dracunculoides, Brugia malayi and Brugia pahangi. Descriptive statistics were used for data analysis. Total infection prevalence with the microscopic evaluation was 77 (37.5 %) and in PCR test was 94 (45.8 %). The most common species of canine filarial parasite identified in this study was D. immitis 54 (57.4 %) followed by Acanthocheilonema species 40 (42.6 %). The molecular evidence on the sequence of the ITS-2 region provided strong evidence that the canine microfilariae discovered in this study belong to a novel species of Acanthocheilonema. Information about infection prevalence helps us to improve disease management practices in the studied area, apply new hygiene policy and reduce extra costs of therapeutic agents and PCR is a quick and accurate molecular genetics method for detection of filarial species.