This study provides information on habitat selection by the threatened Murray cod Maccullochella peelii peelii at two spatial scales in the Ovens and Murray Rivers in south-eastern Australia. Both adult (>450 mm total length, LT) and age 0 year (<150 mm LT) M. p. peelii selected macro and microhabitats based on structural variables. At the macrohabitat scale, adults selected channel habitats in the river, floodplain channels at high floods and within Lake Mulwala, whereas the floodplain proper was avoided. Adult and age 0 year fish selected similar microhabitats regardless of site or hydrologic conditions, and selection was primarily influenced by the presence of higher loadings of structural woody habitat, higher c.v. in depth, more overhanging vegetation, shallower comparative depths and lower water velocities, closer to the bank. Age 0 year M. p. peelii appeared to select shallower habitats with greater amounts of structural woody habitat, closer to the river bank than adult fish.