Onion bulbs (Allium cepa L.) can be stored for up to 12 months to ensure their availability all year, but one of the limiting factors is decay caused by blue mould fungi. Postharvest development of blue mould is not only economically important, but also poses a health hazard due to mycotoxin contamination. Onion bulbs of different yellow and red cultivars with blue mould symptoms were collected from three storage facilities in Serbia. Pathogenic isolates were identified and characterized based on their molecular (partial β‐tubulin gene), morphological (micro‐ and macromorphology, and colony growth) and biochemical properties (analyses of indole metabolites via Ehrlich test). Three Penicillium species were identified: P. polonicum, P. glabrum and P. expansum. Virulence on inoculated onion bulbs varied significantly within isolates of P. glabrum, but the most virulent isolate of P. polonicum and P. glabrum did not differ, nor did they differ from an isolate of P. expansum. Variability in virulence of individual P. glabrum isolates corresponded to differences in their molecular and macromorphological characters. P. glabrum and P. expansum were identified for the first time as causal agents of onion bulb decay in Serbia. Data from this investigation provide insight into diversity of economically important and possibly toxigenic blue mould fungi which brings attention to their presence in storage facilities and therefore the necessity of the application of prevention measures.