The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomised by the freshwater fish Carassius carassius, which is in decline across much of its European range. Restriction site associated DNA sequencing (RADseq) is increasingly used for such applications, however RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. This trade-off has previously been examined using simulation studies, however, empirical comparisons between these markers, especially in a phylogeographic context, are lacking. Here, we compare the results from microsatellites and RADseq for the phylogeography of C. carassius to test whether it is more advantageous to genotype fewer markers (microsatellites) in many samples, or many markers (SNPs) in fewer samples. These datasets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns; showing the existence of two previously unidentified C. carassius lineages in Europe; one found throughout northern and central-eastern European drainages, and a second almost exclusively confined to the Danubian catchment. These lineages have been isolated for approximately 2.15 M years, and should be considered separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with Approximate Bayesian Computation to show that the postglacial colonisation routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology.