BACKGROUND: Proliferation and expansion of security risks necessitates new measures to ensure authenticity and validation of GMOs. Watermarking and other cryptographic methods are available which conceal and recover the original signature, but in the process reveal the authentication information. In many scenarios watermarking and standard cryptographic methods are necessary but not sufficient and new, more advanced, cryptographic protocols are necessary. RESULTS: Herein, we present a new crypto protocol, that is applicable in broader settings, and embeds the authentication string indistinguishably from a random element in the signature space and the string is verified or denied without disclosing the actual signature. Results show that in a nucleotide string of 1000, the algorithm gives a correlation of 0.98 or higher between the distribution of the codon and that of E. coli, making the signature virtually invisible. CONCLUSIONS: This algorithm may be used to securely authenticate and validate GMOs without disclosing the actual signature. While this protocol uses watermarking, its novelty is in use of more complex cryptographic techniques based on zero knowledge proofs to encode information.