Genotyping non-invasively collected samples is challenging. Nevertheless, genetic monitoring of elusive species like the European wildcat (Felis silvestris silvestris) mainly relies on such samples. Wildcats are likely threatened through introgression with domestic cats (F. silvestris catus). To determine introgression based on single cat hairs, we developed a 96.96 Fluidigm single nucleotide polymorphism (SNP) genotyping array chip. To estimate the accuracy of this method, we compared genotypes of 17 cats called with both Sanger sequencing and Fluidigm. When Sanger sequencing genotypes were considered as a reference, the genotyping error rate with Fluidigm was 0.9 %. We subsequently compared 16 hair samples to tissue samples of the same individual. When the tissue samples were used as a reference, the genotyping error rate in hair samples was 1.6 %. This low error rate allowed reliable recognition of individuals and correct assessment of introgression levels. Thus, the genotyping method presented in this paper is suitable for non-invasively collected samples. It will help conservationists to monitor the introgression rate in wildcat populations based on non-invasive hair sampling and subsequently to conduct effective conservation measures.