The modern cryptography is based on information theory in nature. Current cryptosystems rely on mathematics, which take information processing as transformation of numbers or characters. I.e., plaintext, key and crypto text are in the same information level or logical level. Only "one-time pad" system has been proved information-theoretical secure, the rest are computational secure. In fact, the information that we can "see", whatever characters, symbols, numbers or images, and whatever on paper or on screen, is composed of dots distributed in 2-D space. However, modern cryptosystems take information as computable numbers or characters, and simplify the 2-D structure of numbers or characters as one dimension information structure. Here we show that a virtual genome-based cryptosystem (VGC) is a new cryptography based on system theory with many new properties different from that of previous cryptography based on information theory. We design a 2-D structure virtual DNA micro array chip (VDMC), where microdots are corresponding to virtual genes in virtual genome database (VGDB), which DNA sequences are randomly generated. When information is written on VDMC, microdots are selected and marked to compose characters, symbols, numbers or images, and the corresponding virtual genes are determined. A short sequence which is unique in VGDB was selected from the virtual gene, and the uniqueness is ensured by BLAST or other string matching algorithms. Then, the selected microdots on VDMC to compose the information are encrypted into short DNA sequences in VGDB. Decryption is just to use short DNA sequences as queries to BLAST against VGDB and find out virtual genes which have identical homolog with the queries, the corresponding microdots were marked on VDMC, and then the plaintext information can be recognized. As a convenient and secure cryptosystem, VGC can be applied in all areas of information security.