Fish remains are a common component of coastal and inland archaeological assemblages from Australia and the Pacific Islands. Physical reference collections are the primary tool that researchers use to taxonomically identify fish bones but given the high biodiversity of fishes in this region, collections are frequently not complete at the genus- and species-level. Adjunct resources, such as online photograph repositories of fish bone reference collections and illustrated technical guides, provide useful supplementary aids. However, such 2D photographs and illustrations offer fixed perspectives of the bone and do not allow for ready manipulation and detailed examination of the specimen. Here, we introduce Fishboneviz, the first open access 3D fish bone reference collection, which was developed to reduce inequitable access to physical reference collections in line with the FAIR principles of data management (findable, accessible, interoperable, reusable). A ‘best-practice’ methodology was established to facilitate fast and effective segmentation (i.e. isolate regions of interest such as elements) of fish Computed Tomography (CT) scans. This way, fish bone elements of interest were segmented to allow digital manipulation and viewing of the complete element. To examine the effectiveness of the approach, image segmentation procedures were applied to a representative sample of 10 bone elements per fish: dentary, premaxilla, maxilla, articular, quadrate, hyomandibular, opercle, preopercle, last precaudal vertebra, and first caudal vertebra. For species within the family Labridae, the three pharyngeal grinding plates were also segmented. These elements were selected as they represent different regions of the skeleton, variable morphologies, and commonly recovered elements from archaeological sites. To date, the collection contains the skeletal elements of 26 fish species (18 families). In the future, it is hoped that the collection will be further expanded by a broader network of interested collaborators to ensure it grows according to the changing needs of research and teaching communities.