In this thesis I develop, apply, and show how genetic methods of speciation can be used in the identification of archaeological fish bones. I assess the feasibility of applying genetic speciation methods with case studies from southeast Queensland sites and the Greek island of Youra. I have optimised methods and developed the utility and understanding of how such methods can be applied. Basic issues associated with genetic speciation of archaeological fish bones are investigated. I demonstrate that diagenesis and taphonomic issues play a major role in the successful application of genetic methods. I also show that there is a need to scrutinise sequence data at the analytical and interpretory level. Furthermore, I argue that there is a need for caution and understanding of site taphonomy and diagenesis before associating genetic results with specific samples.