Trout cod (Maccullochella macquariensis, Cuvier) is a critically endangered species that now only occurs naturally in a 200 km reach of the Murray River in south-eastern Australia. An assessment of its habitat use was undertaken using radio telemetry to test the assumptions underlying conservation strategies for the species. Trout cod were more likely to be observed in deeper water associated with the low-flow channel. The importance of large wood habitat was dependent on its location within the river channel. In narrow river sections trout cod utilised location where large wood was abundant. In other locations, large wood was associated with deep scour pools that were utilised by trout cod. Our results support rehabilitation of large wood habitat in streams where this was a natural feature as part of the recovery program for this species.