Eleven species of common fungi from compost were analysed for their content of ergosterol and phospholipid fatty acids (PLFAs) after growth on agar media. Mean content of ergosterol was 3.1 mg g(-1) dw of fungal mycelium (range 1-24 mg g(-1) dw). Total amount of PLFAs varied between 2.6 and 43.5 mumol g(-1) dw of fungi (mean 14.9 mumol g(-1) dw). The most common PLFAs were 16:0,18:2omega6,9 and 18:1omega9 comprising between 79 and 97 mol% of the total amount of PLFAs. The PLFA 18:2omega6,9, suggested as a marker molecule for fungi, comprised between 36 and 61 mol% of the total PLFAs in the Ascomycetes, between 45 and 57 mol% in the Basidiomycetes and 1222 mol% in the Zygomycetes. There was a good correlation between the content of the two fungal marker molecules, ergosterol and the PLFA 18:2omega6,9, with a mean content of 1 mg ergosterol being equivalent to 2.1 mumol of 18:2omega6,9. Based on results from the fungal isolates, conversion factors were calculated (5.4 mg ergosterol g(-1) biomass C and 11.8 mumol 18:2omega6,9 g(-1) biomass Q and applied to compost samples in which both the ergosterol and the PLFA 18:2omega6,9 content had been measured. This resulted in similar estimates of fungal biomass C using the two marker molecules, but was three to five times higher than total microbial biomass C calculated using ATP content in the compost. This could partly be explained by the fact that both of the markers used for fungal biomass are cell membrane constituents. Thus, the ergosterol and the PLFA content were related to the hyphal diameter of the fungi, where fungi with thinner hyphae had higher ergosterol concentrations than fungi with thicker hyphae. This could also partly explain the large interspecific variation in content of the two marker molecules. (C) 2003 Elsevier Ltd. All rights reserved.