Efforts to taxonomically delineate species are often confounded with conflicting information and subjective interpretation. Advances in genomic methods have resulted in a new approach to taxonomic identification that stands to greatly reduce much of this conflict. This approach is ideal for species complexes, where divergence times are recent (evolutionarily) and lineages less well defined. The California Roach/Hitch fish species complex is an excellent example, experiencing a convoluted geologic history, diverse habitats, conflicting species designations and potential admixture between species. Here we use this fish complex to illustrate how genomics can be used to better clarify and assign taxonomic categories. We performed restriction-site associated DNA (RAD) sequencing on 255 Roach and Hitch samples collected throughout California to discover and genotype thousands of single nucleotide polymorphism (SNPs). Data were then used in hierarchical principal component, admixture, and FST analyses to provide results that consistently resolved a number of ambiguities and provided novel insights across a range of taxonomic levels. At the highest level, our results show that the CA Roach/Hitch complex should be considered five species split into two genera (4 + 1) as opposed to two species from distinct genera (1 +1). Subsequent levels revealed multiple subspecies and distinct population segments within identified species. At the lowest level, our results indicate Roach from a large coastal river are not native but instead introduced from a nearby river. Overall, this study provides a clear demonstration of the power of genomic methods for informing taxonomy and serves as a model for future studies wishing to decipher difficult species questions. By allowing for systematic identification across multiple scales, taxonomic structure can then be tied to historical and contemporary ecological, geographic or anthropogenic factors.