North American river sturgeons of the genus Scaphirhynchus include three species: S. platorynchus, S. albus and S. suttkusi that live in the Missouri, Mississippi, and Mobile basin. All species of Scaphirhynchus are threatened, endangered or critically endangered due to a combination of factors including of habitat loss and over-harvesting. Genetic tools have been applied for conservation studies in this group, however, the tetrapolyploid nature of the genome of these species have brought a huge challenge to development of nuclear markers for these species and limited knowledge that could be obtained, such as the phylogenetic intrarelationships and population genetics of this genus. Moreover, unintentional hybridization arose from two species of Scaphirhynchus (S. platorynchus and S. albus) that share the same spawning space. To address the problem of species identification and provide genetic markers for population genetic studies on Scaphirhynchus, we developed a bioinformatics pipeline to find SNP markers, based on comparison between single-copy loci of diploid gar and two released autotetraploid genomes of Acipenseriformes. We found 77 SNPs at single-copy loci and 642 SNPs at double-copy loci after filtering. Both the single-copy and double-copy loci supported the same phylogenetic relationship among the three species, in which S. albus and S. platorynchus were more closely related to each other than either of them to S. suttkusi. The principal component analysis using these SNPs also showed that S. albus and S. platorynchus were close to each other. The SNP markers developed in this study should facilitate further researches on population genetics and conservation of the Scaphirhynchus sturgeons.