To assist the management of the critically endangered woylie (Bettongia penicillata ogilbyi), a quantitative study of its diet was conducted across five of the larger subpopulations in south-western Australia. There was a close match between dietary composition established from foregut contents and faecal pellets. Woylies were predominantly mycophagous in all subpopulations, but consumed a broad diet including invertebrates, seeds and other plant material. Individuals in a high-density, fenced subpopulation ate significantly less fungi than free-ranging animals from lower-density subpopulations. Dietary composition did not vary significantly amongst subpopulations in the Upper Warren region, where a range of population densities was observed. Altogether, 79 fungal spore classes were identified, including at least 15 genera from 14 families. Sampling across one year showed that fungi made up a larger fraction of the diet in autumn or winter, and greater diversities of fungi were consumed at these times than at other times of year. This information is essential to provide valuable ecological context for effective population management of woylies, as well as identification and conservation of important habitats.