DNA barcoding has become a widely used and valuable tool in taxonomic research during the past three decades and its application is expanding to fields such as wildlife forensics (e.g. anti-poaching actions). One of the major advantages of DNA barcoding is that it allows for species identification from largely incomplete, deformed or cooked samples and even from traces of biological material. Cyprus is a well-known biodiversity hotspot, the island avifauna comprising around 400 species, 117 of which are listed in Annex I of the Birds Directive (2009/147/EC). Each year on average, 2.3 million individuals (mainly small migratory birds) are trapped illegally on the island and often served at restaurants. Consequently, reliable identification of specimens from processed tissues can be crucial for undertaking legal actions. Herein DNA barcoding of the large majority of bird species resident in Cyprus plus several migrants that were illegally captured was carried out to support local authorities in their anti-poaching actions. In this study, tissue from 103 specimens representing 81 bird taxa were sampled and a 648-bp long fragment of the Cytochrome Oxidase subunit Ι (COI) gene was targeted using a combination of standard, nested and semi-nested PCR depending on the condition of the tissue at hand. Sequences were obtained from all investigated samples and a total of 92 haplotypes was recovered. Phylogenetic reconstructions returned a pattern of relationships among taxa largely compatible with known avian phylogeny. Furthermore, diagnostic polymorphisms within the genus including one of the main targeted species, Sylvia atricapilla, were found. In conclusion, an avian genetic dataset is now available for the law enforcement authorities to identify specimens either confiscated (even when morphologically deformed or cooked) during raids in restaurants and in other premises suspected of serving illegally protected bird species or from trappers.