As urban areas continue to expand and replace natural and agricultural landscapes, the ability to manage and conserve native wildlife within urban environments is becoming increasingly important. To do so we first need to understand species' responses to local-level habitat attributes in order to inform the decision-making process and on-ground conservation actions. Patterns in the occurrence of native terrestrial reptile and small mammal species in 59 sites located in remnant urban habitat fragments of Brisbane City were assessed against local-level environmental characteristics of each site. Cluster analysis, multidimensional scaling ordination, and principal axis correlation were used to investigate relationships between species' occurrences and environmental characteristics. Native reptiles were most strongly associated with the presence of termite mounds, a high amount of fallen woody material, and a moderate amount of weed cover. Native small mammals were most strongly associated with the presence of grass trees (Xanthorrhoea spp.), and both reptiles and small mammals were negatively influenced by increased soil compaction. Significant floristic characteristics were considered to be important as structural, rather than compositional, habitat elements. Therefore, habitat structure, rather than vegetation composition, appears to be most important for determining native, terrestrial reptile and small mammal species assemblages in urban forest fragments. We discuss the management implications in relation to human disturbances and local-level management of urban remnants.