A novel staining and quantification method to investigate changes in intracellular calcium levels [Ca(2+)](i) and morphology in filamentous fungus is presented. Using a simple protocol, two fluorescent dyes, Fluo-4-AM and Cell trace calcein red-orange-AM were loaded into the filamentous fungus Penicillium chrysogenum. The present study investigates the applicability of using Ca(2+)-sensitive dye to quantify and image [Ca(2+)](i) in P. chrysogenum cultures chosen for its potential as an experimental system to study Ca(2+) signalling in elicited cultures. The dye loading was optimised and investigated at different pH loading conditions. It was observed that the fluorophore was taken up throughout the hyphae, retaining cell membrane integrity and no dye compartmentalisation within organelles was observed. From the fluorescent plate-reader studies a significant rise (p<0.001) in the relative fluorescence levels corresponding to [Ca(2+)](i) levels in the hyphae was observed when challenged with an elicitor (mannan oligosaccharide, 150mgL(-1)) which was dependent upon extracellular calcium. Concurrently a novel application of dye-loaded hyphae for morphological analysis was also examined using the imaging software Filament Tracer (Bitplane). Essential quantitative mycelial information including the length and diameter of the segments and number of branch points was obtained using this application based on the three-dimensional data.