The invention relates to information security technology, in particular to a virtual genome-based cryptosystem (VGC). The cryptosystem is provided with two matched keys, of which one is a virtual genome database (VGDB) consisting of random deoxyribonucleic acid (DNA) sequences and the other one is a position table that virtual genes of the VGDB are randomly distributed in a two-dimensional microarray, namely a virtual DNA microarray chip (VDMC). Any plaintext information can be freely written on the VDMC, namely points for forming the plaintext information are selected from the VDMC microarray. The selected points correspond to the virtual genes in the VGDB; small segments of DNA sequences are randomly selected from the virtual genes; and the uniqueness of the small segments of DNA sequences in the VGDB is determined by using a common tool of the bioinformatics, namely a basic local alignment search tool (BLAST), or other character string search algorithms such as a Knuth-Morris-Pratt (KMP) algorithm and the like. A cipher text is combined by the small segments of DNA sequences. The small segments of DNA sequences need only to perform BLAST on the VGDB during decryption, namely the points for forming the plaintext information can be discovered, and the plaintext information can be restored according to the VDMC. Any non-VGDB sequence can be randomly inserted into the cipher text and does not have any influence on the encryption. Thus, the VGC is an excellent information hiding system. In addition, the VGC key can be updated automatically so as to realize an indecipherable one-time-pad system. The cryptosystem is used for real-time quick secret information communication, digital signature and identity authentication.