Intraspecific diversity is a fundamental facet of biodiversity allowing species to adapt to environmental changes. Preserving intraspecific diversity should hence be a main conservation target, although attempts to identify priority conservation areas for intraspecific diversity remain scarce. Using molecular data on six freshwater fish species sampled at a large spatial scale, we determined hot- and cold-spots of genetic diversity, and identified priority conservation areas using a systematic conservation planning approach. We demonstrated that the systematic conservation planning of intraspecific diversity is feasible. However, we found poor levels of congruency and surrogacy among conservation solutions found for each species, indicating that the conservation of intraspecific genetic diversity should be species-specific. This was because of the strong among-species incongruences in hot- and cold-spots of genetic diversity. Our study demonstrates the usefulness of systematic conservation planning for preserving intraspecific diversity, and it provides guidelines to identify priority conservation areas for intraspecific genetic diversity.