The mechanism of toxicity of alkyltributylphosphonium chlorides [P 4 4 4 n ]Cl (n = 1, 3–8, 10, 12 or 14) in conidia of the filamentous fungus Aspergillus nidulans is reported. Systematic elongation of one of the alkyl substituents resulted generally in higher toxicity, as defined by their inhibitory and lethal effects. In this study, fluorescence microscopy is proposed as a direct method for assessing the impact of ionic liquids on the plasma membrane integrity. Data were complemented by microscopic evaluation of the conidia cell wall and morphology. The higher toxicity of phosphonium ionic liquids carrying long alkyl substituents is most likely due to their strong interaction with the conidia cellular boundaries.