Inspired by information processing and communication of life based on complex molecular interactions, some artificial (bio)chemical systems have been developed for applications in molecular information processing or chemo/biosensing and imaging. However, little attention has been paid to simultaneously and comprehensively utilize the information computing, encoding, and molecular recognition capabilities of molecular-level systems (such as DNA-based systems) for multifunctional applications. Herein, a graphene-based steganographically aptasensing system was constructed for multifunctional application, which relies on specific molecular recognition and information encoding abilities of DNA aptamers ( Aeromonas hydrophila and Edwardsiella tarda-binding aptamers as models) and the selective adsorption and fluorescence quenching capacities of graphene oxide (GO). Although graphene-DNA systems have been widely used in biosensors and diagnostics, our proposed graphene-based aptasensing system can not only be utilized for fluorescence sensing and in vivo imaging of fish pathogens ( A. hydrophila and E. tarda), but can also function as a molecular-level logic computing system where the combination of matters (specific molecules or materials) as inputs produces the resulting product (matter level) or fluorescence (energy level) changes as two outputs. More importantly and interestingly, our graphene-based steganographically aptasensing system can also serve as a generally doubly cryptographic and steganographic system for sending different secret messages by using pathogen-binding DNA aptamers as information carriers, GO as a cover, and a pair of keys, that is, target pathogen as a public key, the encryption key used to encode or decode a message in DNA as a private key. Our study not only provides a novel nanobiosensing assay for rapid and effective sensing and in vivo imaging of fish pathogens, but also demonstrates a prototype of (bio)molecular steganography as an important and interesting extension direction of molecular information technology, which is helpful in probably promoting the development of multifunctional molecular-level devices or machines.