The maintenance of biodiversity is a fundamental priority in wildlife conservation. Analysis of key threats can help to identify priority areas and species for management. Chondrichthyans have their highest biodiversity in the Indo-West Pacific and endemism is particularly high for this group in Australia, with almost 50% of the species being found within Australia’s EEZ. Fishery impacts are recognized as a threat not only to target species populations, but also to by-catch species. According to IUCN Red Lists, of the 322 Chondrichthyans described in Australian waters, over 200 species have by-catch and fisheries listed as major threat. Moreover, the choice of priorities for conservation can be undermined by inaccurate catch records or driven to more charismatic species. In more recent years, agencies are implementing ecological knowledge to manage fisheries, and this type of approach is essential when issues like by-catch of undesired or protected species are involved. One of the many aspects of this approach is based on the spatial distribution of species and the impacts that influence aspects of population dynamics such as survivorship. In this study we tested if it is possible to highlight priorities of conservation based on spatial overlap between species and fisheries and the weight of exploitation. Therefore, we developed the Fisheries Interaction Index (FII) and explored the relation between FII and a standard indicator formally established. The method was applied to by-catch Chondrichthyan and target species stocks of the Southern and Eastern Scalefish and Shark Fishery Sector (SESSF) of Australia’s Exclusive Economic Zone. Furthermore, we compare our results with reported IUCN’s Red List Categories of the assessed species.