Phytophthora cinnamomi is a soil-inhabiting ‘water mould’ that is pathogenic to many native plant species in Australia, and has been shown to alter plant species abundance and richness, as well as the structure of vegetation in sclerophyllous vegetation. This study investigated the effects of P. cinnamomi-induced vegetation disturbance and habitat degradation on microhabitat associations of small mammals in a coastal heathland in southern Australia. Seven small mammal species were trapped in a P. cinnamomi-infested heathland community over four years. Trap stations were classified into three disease classes (non-diseased, active disease and post-disease) and structural and floristic aspects of the vegetation were recorded at each station. The mean number of species captured was greatest in non-diseased areas and least in post-disease areas. The total capture frequency of small mammals was lower in post-disease areas except where they were covered by thick stands of tall tea-tree (Leptospermum sp.). Combined small mammal captures were associated with thick vegetation and floristic factors. Captures of Antechinus agilis, Rattus fuscipes, Rattus lutreolus and Sminthopsis leucopus were greatest in non-diseased vegetation and were less frequent in areas of diseased vegetation. A. agilis and R. fuscipes captures were correlated with a floristic factor associated with non-diseased vegetation, while R. lutreolus was associated with structural factors, preferring thick vegetation. The impact on Cercartetus nanus and Isoodon obesulus could not be assessed owing to low captures of these species. Modification of vegetation structure and floristics associated with P. cinnamomi infestation is having a significant impact on the habitat utilised by the small mammal communities in the area. This impact highlights the need to identify and protect those areas that remain free of P. cinnamomi infestation. Continued spread of the pathogen will reduce the area of suitable small-mammal habitat able to support the diverse communities of the eastern Otway Ranges, Victoria, Australia.