Genetic pollution of a native species through hybridization with an invasive species poses an insidious conservation threat. To expose genetic pollution, molecular methods employing multilocus data are required. We present a case study of genetic pollution via hybridization of a native crested newt species, Triturus cristatus, by the invasive T. carnifex on the Veluwe in the Netherlands. We sequenced 50 nuclear markers by next generation sequencing and one mitochondrial marker by Sanger sequencing for four populations from the native range of both parent species and eleven ponds on the Veluwe. We use three population genetic approaches (HIest, BAPS and Structure) to determine the genetic composition of the Veluwe newts based on all nuclear markers, a subset of 18 diagnostic markers and the complementary 32 non-diagnostic markers, with and without parental populations. BAPS underestimates genetic pollution, whereas Structure is comparatively accurate compared to HIest, although Structure’s relative advantage ... : Triturus transcriptome-based gene models in FASTA formatTriturus transcriptome-based gene models in FASTA formatFASTA.zipRaw Ion Torrent reads in FASTQ formatRaw Ion Torrent reads in FASTQ formatFASTQ.zipBWA alignments in SAM formatBWA alignments in SAM formatSAM.zipRaw SNP reports in VCF formatRaw SNP reports in VCF formatVCF.zipScripts associated with the bioinformatics pipelineScripts associated with the bioinformatics pipelineScripts_Ion_Torrent_Triturus.zipInput files for the data simulationInput files for the data simulationData Simulation input.zipInput files for HIest, Structure and BAPSInput files for HIest, Structure and BAPSHIest, Structure and BAPS input.zipND4 SPF filesND4 SPF filesND4.SPFFiltered SNP report used to construct consensus sequencesFiltered SNP report used to construct consensus sequencesStatistics.zip ...