Aerosol in the size range 0.8–20 μm was characterized according to optical equivalent diameter, <i>D</i><sub><i>P</i></sub>, morphology and the presence of biological material, the latter determined by recording fluorescence excited by ultraviolet light pulses at two different wavelengths. Single-particle measurements were performed within and subsequently above a tropical rainforest in Borneo, Malaysia, in June and July 2008. In both locations the aerosol number size distribution exhibited a primary biological aerosol (PBA) mode sized 2 μm<<i>D</i><sub><i>P</i></sub><20 μm and much larger in number within the forest than above it, suggesting the PBA originates below the canopy. PBA was observed to dominate the total number at <i>D</i><sub><i>P</i></sub>>2 μm and possessed a wider morphological range than non-PBA. It also accounted for around 80% of the total number in the understory and 40% of the total number above canopy. Canopy transmission efficiencies for the total aerosol number and PBA are calculated to be 0.48±0.19 and 0.31±0.15 respectively, with the former appearing to peak during the daytime because of a lack of PBA emission below the canopy.