PM2.5 emissions and polycyclic aromatic hydrocarbons (PAHs) in PM2.5 of pure biodiesel derived from different feedstocks were investigated and compared with diesel fuel. B100-1 (soyabean oil derived), B100-2 (waste oil derived) and diesel fuel were tested on a diesel engine bench at four operating conditions, including two steady speeds of different loads. The fine particles were collected by fiber quartz filter and particle phase PAHs were analyzed by GC-MS. Compared with diesel fuel, biodiesel decreased PM2.5 emission rates with a maximal reduction rate of 37.3% at operating modes of high loads, while increased PM2.5 emission rates at low loads. PAHs emission rates from biodiesel decreased at all tested modes, with a maximal reduction rate of 77.6%. The emission rates of PM2.5 and PAHs of B100-2 were 14.7% and 17.8% times of B100-1. Low molecular weight PAHs dominated in the emission of three fuels with phenanthrene as maxima and 2-ring and 3-ring PAHs accounted for more than 50% of the total PAHs. Toxic equivalence of PAHs emissions of biodiesel was decreased greatly compared with that of diesel.