Holstein-Friesian (HF) is a cosmopolitan breed distributed in more than 150 countries. It represents a large metapopulation with intensive gene flow, realised mainly through artificial insemination and the intensive use of the popular „star“ bulls. The breed is known for its superiority in milk yield, production efficiency and black and white coat color. In contrast to the enormous size of the census population, which exceeds nine million animals in the U.S. alone, the genetic diversity of this highly commercialised breed is surprisingly low, necessitating genetic monitoring, especially of subpopulations in individual countries. Our main objective in this study was to analyze genomic diversity (estimated by genomic inbreeding and effective population size) and population structure (relationship to other subpopulations) of the subpopulation from the Czech Republic and, based on high-throughput SNP array genotypes. We analysed 2178 animal samples (32,865 autosomal SNP) from 12 sub-populations and the Simental cattle breed (98 animals), which represents an outlier population. Czech bulls showed high genomic inbreeding (FROH>2Mb=0.133), well above the inbreeding level of Czech cows (FROH>2Mb=0.091), with particularly high recent inbreeding (ROH>8Mb). Unexpectedly, the estimated effective population size (NeLD) was relatively high, ranging from 202 (GONE) to 283 (NeEstimator v2), depending on the estimation algorithm. Our phylogenetic analyses showed that the Czech HF belonged to the „core metapopulation HF „, together with Belgian, British, Canadian, Dutch, French, German, and USA subpopulations, which was separated from the Swiss, Irish, and Croatian subpopulations. We also showed that Czech AI bulls differed slightly from cows, especially in genes affecting meat and carcass. Our results have defined the population structure of the Czech HF and indicate the potential problems of increased inbreeding due to selection of AI bulls.