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Ticks are a large group of blood-feeding arthropods that transmit multiple human and animal pathogens and are hence of importance to public health. The tick Haemaphysalis longicornis is associated with the transmission of multiple human pathogens in Asia, and recently found invading to the United States. Here, we report the sequencing, assembly and annotation of the 3.16 gigabase genome of this species, which is larger than the previous assembled one. The present Haemaphysalis longicornis genome was characterized by 6519 scaffolds, 24,189 protein-coding genes and a high proportion of simple sequence repeats (54.72%). By genomic assembly and comparative genomic analysis, we characterized the key genes that play essential roles in iron metabolism, detoxification, and freeze tolerance of H. longicornis. Furthermore, a total of 79 endogenous viral elements were identified within the genome, which might have had a considerable impact on its evolution. Decoding the H. longicornis genome not only provides insight into the genetic underpinnings of specific biological processes but also offers the basis for the subsequent integrated control of ticks and tick-borne diseases. • A high quality of 3.16 gigabase genome of Haemaphysalis longicornis were assembled. • The key genes mediating the requisite biological traits of H. longicornis were characterized. • A total of 79 endogenous viral elements were identified within the H. longicornis genome. • The genome annotation are useful for future control of ticks and tick-borne diseases. [ABSTRACT FROM AUTHOR]