Translocating threatened ecosystem engineers may offer the dual benefit of contributing to species conservation and ecosystem restoration. Boodies (burrowing bettong; Bettongia lesueur) and woylies (brush-tailed bettong; Bettongia ogilbyi) are threatened mycophagous marsupials known for their crucial role in ecosystem health through fungal dispersal and bioturbation. As part of restoration efforts across Australia, these bettong species are frequently targeted for translocations, where a better understanding of their fungal dietary requirements is essential for ensuring their resource requirements are met and in predicting their ecological contributions to recipient ecosystems. Here, we used DNA metabarcoding to study the fungal diets of boodies and woylies from 90 scat samples collected across five sites spanning Mediterranean-type to arid climates. DNA metabarcoding identified 379 fungal amplicon sequence variants (ASVs) from scat samples, of which 82 ASVs were identified as macrofungi, likely to be deliberately consumed by boodies and woylies. We found that both species of bettongs demonstrated similar fungal dietary diversity profiles, with fungi from the Pezizaceae family consistently prevalent across all sites. However, potentially opposing associations to aridity index were observed. Analysis of functional guilds revealed some redundancy in dispersal roles between boodies and woylies when co-occurring. However, subtle differences in their consumption of secondary fungal resources may promote the dispersal and persistence of a broader range of fungal taxa. Our study reinforces the prevalence of truffle-like fungi in mycophagous mammal diets and suggests that minor dietary differences may aid in reducing competition while providing some complementary ecosystem benefits. We recommend that future translocations be informed by comprehensive resource and carrying capacity assessments of the translocation site, with releases strategically timed for post-rainfall periods and monitored across complete drought cycles to ensure successful establishment of boodies and woylies.