The American paddlefish, Polyodon spathula (Walbaum), is an endangered acipenserid fish. Its wild populations are supplemented with stocking material that is obtained by conducting artificial spawning in aquaculture conditions. When fish are bred in captivity, it is important to select breeding pairs that will produce the most genetically diverse progeny, since this permits maintaining the fitness of wild populations. Breeding pairs of land animals are selected successfully based on the polymorphism of their microsatellite loci. This theoretical paper asks how to adapt this technique to fish so that American paddlefish spawners can be paired with the aim of producing restocking material in aquaculture that maintains genetic variation. To test our calculating techniques, we used actual data on the polymorphism of the microsatellites from paddlefish broodstock at the Pogorze fish farm (Poland). The data enabled us to do calculations that showed which spawner pairs would create the most genetically diverse offspring and how to assemble sets of spawning pairs that would be best for maintaining genetic variation. The method presented in this paper can be used for breeding fish in aquaculture to help conserve species. It could also be used in a computer program which would automate calculations and present them in easy-to-read tables and graphs.