The spatial distribution and density of scientists can have important implications for key aspects of scientific processes, such as innovation, networking, rates of knowledge exchange and success in large competitive grants. In this paper, we examine the research output of different research organizations and universities in Australia, with the aim of identifying hotspots of ecological research and how these hotspots have changed over the last 20 years. We used publications from 10 reputable peer-reviewed international journals as a measure of research output. We identified a number of ecology hotspot clusters. Some clusters have developed significantly over the last 20 years, while others have declined in output over time. The University of Sydney, University of Queensland, James Cook University and Melbourne University had the largest output levels among universities. Results also showed large increases in output over the last 5-year period (2006–2010), possibly because of the impending introduction of the Excellence in Research for Australia.