The present study focuses on the Belgian Milk Sheep in Flanders (Belgium) and compares its genetic diversity and relationship with the Flemish Sheep, the Friesian Milk Sheep, the French Lacaune dairy sheep and other Northern European breeds. For this study, 94 Belgian Milk Sheep, 23 Flemish Sheep and 22 Friesian Milk Sheep were genotyped with the OvineSNP50 array. In addition, 29 unregistered animals phenotypically similar to Belgian Milk Sheep were genotyped using the 15K ISGC chip. Both Belgian and Friesian Milk Sheep as well as the East Friesian Sheep were found to be less diverse than the other seven breeds included in this study. Genomic inbreeding coefficients based on runs of homozygosity (ROH) were estimated at 14.5, 12.4 and 10.2% for Belgian Milk Sheep, Flemish Sheep and Friesian Milk Sheep respectively. Out of 29 unregistered Belgian Milk Sheep, 28 mapped in the registered Belgian Milk Sheep population. Ancestry analysis, PCA and FST calculations showed that Belgian Milk Sheep are more related to Friesian Milk Sheep than to Flemish Sheep, which was contrary to the breeders' expectations. Consequently, breeders may prefer to crossbreed Belgian Milk Sheep with Friesian sheep populations (Friesian Milk Sheep or East Friesian Sheep) in order to increase diversity. This research underlines the usefulness of SNP chip genotyping and ROH analyses for monitoring genetic diversity and studying genetic links in small livestock populations, profiting from internationally available genotypes. As assessment of genetic diversity is vital for long-term breed survival, these results will aid flockbooks to preserve genetic diversity.