Abstract. Bioaerosols pose risks to human health and agriculture and may influence the evolution of mixed-phase clouds and the hydrological cycle on local and regional scales. The availability and reliability of methods and data on the abundance and properties of atmospheric bioaerosols, however, are rather limited. Here we analyze and compare data from different real-time ultraviolet laser/light-induced fluorescence (UV-LIF) instruments with results from a culture-based spore sampler and offline molecular tracers for airborne fungal spores in a semi-arid forest in the southern Rocky Mountains of Colorado. Commercial UV-APS (ultraviolet aerodynamic particle sizer) and WIBS-3 (wideband integrated bioaerosol sensor, version 3) instruments with different excitation and emission wavelengths were utilized to measure fluorescent aerosol particles (FAPs) during both dry weather conditions and periods heavily influenced by rain. Seven molecular tracers of bioaerosols were quantified by analysis of total suspended particle (TSP) high-volume filter samples using a high-performance anion-exchange chromatography system with pulsed amperometric detection (HPAEC-PAD). From the same measurement campaign, Huffman et al. (2013) previously reported dramatic increases in total and fluorescent particle concentrations during and immediately after rainfall and also showed a strong relationship between the concentrations of FAPs and ice nuclei (Huffman et al., 2013; Prenni et al., 2013). Here we investigate molecular tracers and show that during rainy periods the atmospheric concentrations of arabitol (35.2 ± 10.5 ng m⁻³) and mannitol (44.9 ± 13.8 ng m⁻³) were 3–4 times higher than during dry periods. During and after rain, the correlations between FAP and tracer mass concentrations were also significantly improved. Fungal spore number concentrations on the order of 10⁴ m⁻³, accounting for 2–5 % of TSP mass during dry periods and 17–23 % during rainy periods, were obtained from scaling the tracer measurements and from multiple analysis methods applied to the UV-LIF data. Endotoxin concentrations were also enhanced during rainy periods, but showed no correlation with FAP concentrations. Average mass concentrations of erythritol, levoglucosan, glucose, and (1 → 3)-β-D-glucan in TSP samples are reported separately for dry and rainy weather conditions. Overall, the results indicate that UV-LIF measurements can be used to infer fungal spore concentrations, but substantial development of instrumental and data analysis methods appears to be required for improved quantification.