The gene pool of indigenous Faroe Islands Cattle is strongly affected by crossing with Norwegian Red. In this study, the genetic structure in 191 animals representing five North European cattle breeds (Faroe Islands, Icelandic, Blacksided Troender, Western Fjord and Norwegian Red) and the genetic admixture in the contemporary Faroe Islands Cattle at the population and individual level were evaluated using 20 polymorphic microsatellite loci. Only 6.7% of the total genetic variation could be attributed to the differences amongst the breeds. The factorial correspondence analysis based on all allele frequencies could hardly reveal a divergence between Faroe Islands Cattle and Norwegian Red. In addition, a Neighbor-Net tree constructed to examine the allocation of individuals of Faroe Islands Cattle and Norwegian Red provided a detailed interrelationship network for all the 72 animals. An estimation of the population admixture proportion showed a strong genetic contribution by Norwegian Red (47.3%) in the contemporary Faroe Islands Cattle. On the other hand, individual admixture analysis demonstrated that only seven of the individual Faroe Islands Cattle analysed, which also showed more traditional colour patterns, could be assigned to the Faroe Islands Cattle cluster, probably representing the breed's remaining purebred animals. Strategies for preserving the original native genes in Faroe Islands Cattle should be considered in order to prevent the breed from becoming extinct and to strengthen the breed's capability in future breeding programmes.