Babesiosis, caused by parasites of the Babesia genus transmitted by ticks, is a disease that significantly impacts animal and human health worldwide. Understanding the biological aspects related to the pathogenesis of Babesia is critical, given that no vaccine is available to date, and multiple strains of the species are developing resistance to drugs. Advances in sequencing have greatly improved the understanding of the pathogenic dynamics of different species and have provided invaluable information for the search for alternative therapies, management, and perhaps the elimination of the disease. Consequently, this chapter summarizes the main omics findings (genomics, transcriptomics, proteomics, immunomics, and metabolomics) that have been carried out in recent years to understand the biology of Babesia species, emphasizing their usefulness for the search for key molecules in diagnosis, pathogenesis, pathophysiology, and vaccine development. A comprehensive view of the biology of Babesia is provided, and new perspectives for the development of control and treatment strategies are discussed, addressing the challenges and future directions in the fight against babesiosis.