Apicomplexa is a eukaryotic phylum of intracellular parasites with more than 6000 species. Some of these single-celled parasites are important pathogens of livestock. At present, 128 genomes of phylum Apicomplexa have been reported in the GenBank database, of which 17 genomes belong to five genera that are pathogens of farm animals: Babesia, Theileria, Eimeria, Neospora and Sarcocystis. These 17 genomes are Babesia bigemina (five chromosomes), Babesia divergens (514 contigs) and Babesia bovis (four chromosomes and one apicoplast); Theileria parva (four chromosomes and one apicoplast), Theileria annulata (four chromosomes), Theileria orientalis (four chromosomes and one apicoplast) and Theileria equi (four chromosomes and one apicoplast); Eimeria brunetti (24,647 contigs), Eimeria necatrix (4667 contigs), Eimeria tenella (12,727 contigs), Eimeria acervulina (4947 contigs), Eimeria maxima (4570 contigs), Eimeria mitis (65,610 contigs) and Eimeria praecox (53,359 contigs); Neospora caninum (14 chromosomes); and Sarcocystis neurona strains SN1 (2862 contigs) and SN3 (3191 contigs). The study of these genomes allows us to understand their mechanisms of pathogenicity and identify genes that encode proteins as a possible vaccine antigen.