Edible bird’s nest (EBN) is a functional food constructed with swiftlets’ salivary glue. Counterfeit EBN products have been found in the market due to limited supply and high price of genuine EBN. In this article, a method for genetic identification of EBN was developed. The technique is based on sequence of cytochrome b gene in mitochondrial DNA. The sample sequences together with the sequences of swiftlets in GenBank were used to construct phylogenetic trees for genetic identification of samples. This method was applied to 11 EBN samples, one instant EBN soup product from Indonesia, and Huaiji EBN, a counterfeit EBN in some regions of China. Results showed that all the EBN samples and the instant EBN soup were from Aerodramus fuciphagus while the Huaiji EBN sample was from Apus nipalensis. This was consistent with identification based on morphology of the samples. Therefore, this method is a promising tool to identify the species of bird producing a given sample of EBN, and thus could be used to authenticate—that is, distinguish authentic from counterfeit—EBN.