Unprecedented rates of extinction have lead to the development of fields, such as conservation genetics, in an attempt to better understand biodiversity and consequently devise conservation programs to maintain the genetic integrity of species. We discuss the utility and application of conservation genetics, using examples from Australian freshwater crayfish, with a view to applying this methodology to the sole native crayfish species found in Japan, Cambaroides japonicus (De Haan). This species is threatened by the non-indigenous crayfish Pacifastacus leniusculus (Dana) through displacement, competition pressures, and susceptibility to Aphanomyces astaci Schikora (the crayfish plague, carried by the invasive species). Examining the genetic diversity within C. japonicus could allow populations of high conservation priority to be identified (i.e., genetically distinct populations) or, in contrast, show that this species is genetically homogenous. Such genetic continuity may suggest that other conservation methods (e.g., translocations and restocking populations) may be suitable for this species of crayfish. Identifying genetic variability, or lack thereof, is a key step in dictating the future direction of any conservation measures for C. japonicus.