Central to Ecosystem-Based Fisheries Management is the need to conserve biodiversity. However, management agencies responsible for the maintenance of fish and aquatic biodiversity are faced with real uncertainty about what is meant by biodiversity and significant debate around what temporal/spatial scales should be considered in relation to measuring and monitoring biodiversity. The implementation of biodiversity management plans create issues for the various state- and federal-level jurisdictions, such as (i) the need to manage anthropogenic impacts on aquatic ecosystems that are beyond the control of any one level of jurisdiction (e.g. climate change), (ii) Commonwealth initiatives (e.g. Bioregional planning) that have potential to influence the management of biodiversity at the state-level and (iii) human activities that can impact aquatic biodiversity e.g. fishing, securing water supply and coastal development. There is a need for the expert opinions of scientists from the relevant disciplines to be summarized and presented to managers in a way that allows policy-makers to understand what the management of fisheries and aquatic ecosystem biodiversity means in real terms. Scientists need to provide workable options for managers in relation to the measurement and monitoring of aquatic biodiversity. The Australian Society for Fish Biology (ASFB) proposes to facilitate this exchange of information via a dedicated workshop to be held in Fremantle in June 2009 as part of the 8th Indo-Pacific Fish Conference and Australian Society of Fish Biology Conference.