Biodiesel is an important alternative energy in the Thailand Alternative Energy Development Plan (AEDP). Fishermen are one of the government s target groups since they significantly affect the country s economics and consume a large amount of diesel. Two HINO and two GARDNER engines were selected from small fishery boats in order to compare the engine performances when fuelled with biodiesels B5 and B20. The engine performances, after 500-hour operations, were also investigated. The fuel qualities were certified by Department of Energy Business, Thailand Ministry of Energy. The results showed that engine torque of biodiesel B20 was lower than that of biodiesel B5 in the range of 2.40 to 7.54%. This is due to the lower heating value. According to the better lubricity of biodiesel B20, no engine breakdown was observed. It was also reported that engine performances decreased slightly after the 500-hour operation. Therefore, biodiesel B20 is feasible for the real application.