Abstract: To monitor fuel compliance of ships navigating in the Pearl River waters, a UAV sniffer system for monitoring ship exhaust is designed. The UAV is equipped with a mini sniffer sensor and hovers over ships to monitor in real time the concentration of SO₂ and CO₂ they emitted and screens out the ships using high sulfur fuel. The system is tested on-site. The sniffer measurement of sulfur content in fuel is verified by comparing it with the actual content of the fuel oil the monitored ship uses. The system has been practically applied to monitor the compliance of ships with fuel rules and its effectiveness is proved.