Aerosol particle size distributions were measured below and above a tropical rainforest canopy in Borneo, Malaysia, in June/July 2008 using the WIBS-3: a single particle dual channel fluorescence spectrometer. Material in the size range 0.8–20 &mu;m was characterized according to optical equivalent diameter (<i>D</i>_P), morphology and fluorescence at 310–400 nm and 400–600 nm following excitation at 280 nm and 370 nm respectively. Particles fluorescent after both excitations are likely to be fluorescent primary biological aerosol particles (FBAP). <br><br> Measured FBAP number concentration (<i>N</i>_FBAP) at both sites exhibited clear diurnal cycles. The largest variability was observed in the understorey, where <i>N</i>_FBAP reached a minimum of 50–100 L⁻¹ in late morning. In mid afternoon it exhibited strong transient fluctuations as large as 4000 L⁻¹ that were followed by sustained concentrations of 1000–2500 L⁻¹ that reduced steadily between midnight and sunrise. Above the canopy FBAP number ranged from 50–100 L⁻¹ during the daytime to 200–400 L⁻¹ at night but did not exhibit the transient enhancements seen in the understorey. The strong FBAP fluctuations were attributed to the release of fungal spores below the canopy and appeared to be linked to elevated relative humidity. <br><br> The mean FBAP number fraction in the size range 0.8 &mu;m<<i>D</i>_P<20 &mu;m was 55% in the understorey and 28% above canopy. A size mode at 2 &mu;m<<i>D</i>_P<4 &mu;m appears at both sites and is primarily FBAP, which dominated the coarse (<i>D</i>_P&ge;2.5 &mu;m) number concentration at both sites, accounting for 75% in the understorey and 57% above the canopy. In contrast, the concentration of non-fluorescent particles (<i>N</i>_NON) at both sites was typically 200–500 L⁻¹, the majority of which occupied a size mode at 0.8<<i>D</i>_P<1.5 &mu;m. Enhanced understorey <i>N</i>_NON was observed daily in mid-afternoon and also at midday on three occasions: the former coincided with the FBAP enhancements and measured approximately 10% of their magnitude; the latter occurred independently of the <i>N</i>_FBAP diurnal cycle and comprised particles smaller than 2 &mu;m. Particle diameter of 3–5 &mu;m is consistent with smaller fungal spores, though absolute identification of biological species is not possible with the UV-LIF technique. Based on the measured FBAP and non-fluorescent particle abundances and their observed recovery times following rain showers, FBAP originated beneath the canopy while the non-fluorescent material was transported from further away. It is concluded that these separate sources contributed the majority of the aerosol measured by the WIBS-3 at both sites.