Abstract DNA barcoding by Cytochrome Oxidase c Subunit I (COI) has gained a wide popularity in the world as a single species identification method. It has been utilized in many fields e.g. evolution, conservation and forensic. The birds of Oman were not characterized previously through molecular approach. The objective of this study was to use COI barcodes for identification of birds of Oman. A DNA fragment of 910 bp length from the COI was sequenced and analyzed. The total identified species of birds were 69 species. All species, except for three, gave unique barcodes. The col barcoding efficiency was 95.7%. The average intraspecific divergence was 0.34%, while the average interspecific divergence was 19.3%. Some species where found to be polytypic. Significant proportion (11.6%) of the species collected from the ONHM was misidentified based on phonotypical identification. The relatively high intraspecific and interspecific divergence might be due to the different origin of samples in the analysis as most of the birds of Oman are migratory birds. The misidentification of birds could be referred to similar phenotypes among closely related species. More sampling in terms of both species and numbers should be obtained in order to investigate the genetic structure of the birds in the region. Further investigation for certain species (Falco concolor, Falco subbuteo and Lanius meridionalis) is needed. The molecular identification of birds should be emphasized in the museums together with phenotypic identification to avoid mislabeling of the species