Abstract Cities have a major impact on Australian landscapes, especially in coastal regions, to the detriment of native biodiversity. Areas suitable for urban development often coincide with those areas that support high levels of species diversity and endemism. However, there is a paucity of reliable information available to guide urban conservation planning and management, especially regarding the trade-off between investing in protecting and restoring habitat at the landscape level, and investing in programmes to maintain the condition of remnant vegetation at the local (site) level. We review the literature on Australian urban ecology, focusing on urban terrestrial and aquatic vertebrate and invertebrate fauna. We identify four main factors limiting our knowledge of urban fauna: (i) a lack of studies focusing at multiple ecological levels; (ii) a lack of multispecies studies; (iii) an almost total absence of long-term (temporal) studies; and (iv) a need for stronger integration of research outcomes into urban conservation planning and management. We present a set of key principles for the development of a spatially explicit, long-term approach to urban fauna research. This requires an understanding of the importance of local-level habitat quality and condition relative to the composition, configuration and connectivity of habitats within the larger urban landscape. These principles will ultimately strengthen urban fauna management and conservation planning by enabling us to prioritize and allocate limited financial resources to maximize the conservation return.