The Czech Red cattle is a historical local breed of the combined type originating from the mountain regions of Bohemia and Moravia. Like the Harz Red Cattle, it is sometimes being associated with the ancient Celtic Red cattle. The first conservation efforts can be dated back to the beginning of the 20th century. Whole genome sequencing was performed in individuals representing animals with the highest proportion of the original gene pool (the highest value 38%). In parallel, pooled population samples were re-sequenced in order to obtain a survey of the total variability. The Illumina HiSeq technology for 2×150 reads was applied with 10× coverage for individual animals and 30× coverage for the populations of 80 animals.