Abstract: Recognized as the third observation platform, seafloor observatories enable long term, continuous, real time, all weather and multitask scientific observation and become the most remarkable trend in international marine science and technology. This study is aimed to establish a junction box based gateway middleware prior to the back-end server for diverse seafloor observatory monitoring applications. The design manipulates diverse sensor data with communication and processing balance and also gives reference for representing such kind of middleware in the cyberinfrastructure for seafloor observatories. As considering sensor characteristics of data acquisition and data processing for seafloor observatory monitoring, the proposed junction box based gateway middleware is designed with three bridged function modules including data monitor, transaction executer and network responder, to enable real-time data acquisition, data filtering, data interpretation and visualization, database redundancy and storage and control commands configuration. The cyberinfrastructure representation of the gateway middleware is discussed and designed using service-oriented architectures (SOA) and web services. The middleware is built upon the junction box for two-way communication and interoperation to perform efficient and stable applications. The comprehensive middleware design can be easily utilized for general seafloor observatory sensor network surveillance with expansibility and flexibility.