Native animals exploit resources in cities and inhabit anthropogenic structures worldwide. One example of this is the little penguin, Eudyptula minor, population nesting between boulders on the St Kilda breakwater in Melbourne. This population is attracted by safe hiding places, a lack of predators and the presence of prey. However, living close to urbanisation poses many threats to the colony, including boating, lighting, noise and human visitation.We investigated the effects of human disturbance by comparing the number of penguins and breeding sites in the publicly accessible region with those in the restricted region of the breakwater. Penguins and nest sites were not equally distributed along the breakwater, with the mean number of birds and nest sites present per 20-m section in the restricted region significantly greater (typically double) than the number in the publicly accessible region. Although the penguins show a clear preference to nest in the restricted region of the breakwater, their continued presence in the publicly accessible region when nest sites are not limiting indicates that human disturbance is not incompatible with some nesting activity. In a global context these results illustrate some of the benefits and costs to animals that use anthropogenically altered habitats and urban environments.