We established a DNA watermarking system for discriminating transgenic plants. The system contains an encryption algorithm based on a binary system, genetic transformation and a detection algorithm for encrypted DNA watermark sequences using a DNA dot plot. The encryption algorithm converted character strings into nucleic acid sequences through binary digits, and the sequence was designed to be resistant to transition mutations to decipher codes completely. Moreover, the encrypted sequences were capable of taking specific nucleotide sequences in using the algorithmic redundancy of the corresponding DNA. Genetic transformation enables labeling plant genomes with DNA watermarks. The detection algorithm allows finding traces of sequence changes in DNA watermarks, complementing the error protection function of the encryption algorithm. To validate the effectiveness of our DNA watermarking system, we introduced a DNA watermark to the tobacco genome and detected the DNA watermark in PCR products amplified from the genome. This indicates that DNA watermark technology is useful for introducing artificial genetic markers in plant organisms, in particular when several transgenic host plants and transgenes are used. The source codes of the Perl scripts are available in this report.Key words: Binary digits, decoding, encryption, transgenic plant, watermark.Much attention has been paid to DNA watermarks for authentication and identification of organisms (Heider and Barnekow 2007). DNA watermark technology employs DNA sequences with encrypted information to label organisms (Arita and Ohashi 2004;Clelland et al. 1999;Gehani et al. 2000;Heider et al. 2009;Leier et al. 2000;Wong et al. 2003). Recently, DNA watermark technology was tested in an applied study in bacteria and yeast . It was also used to label an artificial genome in a bacterial study (Gibson et al. 2010). Such applications could be useful for plant breeding. Since farms and plant breeding fields are often established as open-ended systems, plants with valuable genetic traits often face the risk of being pirated without a legally valid mark. Tai et al. (2013) proposed that the use of DNA watermarks could facilitate the authentication and annotation of important plant variety rights. However, to our knowledge, utilization of DNA watermark technology in plants has not previously been reported.DNA watermark technologies are generally comprised of three processes: encryption, labeling and detection (Halvorsen and Wong 2012;Jupiter et al. 2010). Encryption embeds a particular message or information within a DNA sequence. In labeling, the DNA sequence containing the encrypted information is assimilated into a target organism by genetic engineering (Chou et al. 2004;Mercenier and Chassy 1988;Newell 2000). In detection, the hidden information is mined and decrypted from the genomic sequences to obtain the original message. The encryption process is the most crucial step in DNA watermarking because it primarily determines the subsequent processes. Several encryption ...