In order to avoid the illegal use of fishing boat fuel A (FBFA) by traveling diesel vehicles (TDVs) in Taiwan, alternatives that are easily distinguished from premium diesel fuel (PDF) were prepared to evaluate their suitability. Two new ingredients, pyrolysis fuel oil (PFO) and residue of desulfurization unit (RDS), were added into FBFA and formed PFO0.5 and RDS0.5, respectively. Along with FBFA, these three fuels were analyzed for their chemical and physical properties. Furthermore, they were used by three fishing boats with different sizes, output powers, and weights. The engine performances and pollutant emissions were examined and monitored. Experimental results show that there are significant differences in appearance between PDF and the two new blended fuels (PFO0.5 and RDS0.5), and thus misuse or illegal use of FBFA could be substantially reduced. The fuel consumption, which is negatively related to the heating value of fuels, is in order of FBFA<PFO0.5=RDS0.5. In contrast with using FBFA in the three fishing boats, using RDS0.5 resulted in a decrease in CO and NO(x) emissions, while the PM emission factors (g bhp(-1) h(-1) and g L(-1)-fuel) were reduced by approximately 36% and 33%, respectively. Owing to the higher total aromatic content in PFO0.5 and RDS0.5, total-PAH concentrations in the exhausts from the three fishing boats using PFO0.5 and RDS0.5 were slightly (1.2 and 1.1 times, respectively) higher than for those using FBFA. Nevertheless, the estimated total BaP(eq) from the three fishing boats using RDS0.5 was 27.5, 19.5, and 8.25% lower than those using FBFA. With using PFO0.5, they were totally different, at 23.5, 2.79, and 2.58% higher. With regard to looking different to PDF, RDS0.5 is superior to PFO0.5, and is thus recommended as a better alternative to FBFA, particularly because it can help lower more emissions of CO, NO(x), PM and BaP(eq).