Abstract: OBJECTIVE To confirm the real identity of imported bird's nest origin species in South-east Asia, the 12S rRNA and Cytb gene sequences from twenty-five bird's nest samples from South-east Asia were determined and analyzed, which including two precious bloody nest sample(yellow nest and bloody nest) collected from the birdnest cave in Malysia. METHODS Twenty five samples without any processing were collected from birdnest cave and birdnest house in Malaysia, Singapore and Vietnam. The genomic DNA directly extracted from bird's nest was used as template to amplify 12S rRNA and Cytb gene sequences by redesigned primers, and then cloned and sequenced. RESULTS All the sequences were BLAST against their homologous sequences in GenBank database and the gene trees were constructed. Based on the species information of swiftlets collected in the sample collection area, these samples were initially identified as Aerodramus fuciphagus and Aerodramus maximus. CONCLUSION The sequence aliment analyses approve that they are the right mitochondrial gene from the Aerodramus species. Combined with the species distribution data and gene sequence information of the original swiftlets, these sequence data acquired by this method can be used to formulate the quality standard of imported bird's nest.