In Australia, the health of our marine, estuarine, and freshwater ecosystems is of critical importance. Each of these aquatic environments play a significant role in our countries ecological, economic, cultural and societal wealth. Burgeoning threats including climate change, resource over-exploitation, invasive animals and diseases, and habitat degradation are just a few of the issues that researchers and managers must consider. To identify the key research priorities using a bottom up process we surveyed researchers, policy makers and academics to determine the research priorities that they perceive as the most important for furthering fish and fisheries research in Australia. The survey responses covered eight thematic fields of study. Preliminary results indicate that fisheries, environment and climate, and resource management were the top three themes respondents posed questions about, followed closely by freshwater ecosystems and biosecurity. Around 70% of respondents were researchers, and representation from all Australian State and Territories was achieved. A follow up consolidation and prioritisation process was undertaken to narrow the broad range of research priorities received and allow for a list of key priorities to be developed. The priorities identified will enable researchers and policy makers to identify critical knowledge gaps, promote collaborative programs (both within and across management jurisdictions), develop novel approaches and technologies, promote resource pooling to achieve common goals, and to improve transparency around decision-making processes.