Southeast Asia is known for its rich diversity of organisms, including parasites and pathogens. Ticks (Arachnida: Ixodida) are parasitic arthropods known to transmit a wide array of pathogens in humans and animals. There are more than 100 species of ticks reported in Southeast Asia. The tropical climate of the region highly favors the survival and reproduction of many tick species. However, knowledge of ticks and tick-borne pathogens in Southeast Asia is scarce compared to that in other parts of the world. Research conducted on ticks and tick-borne diseases (TBDs) are limited to those affecting animals. Despite the recognition of many TBDs as emerging zoonotic diseases, much is still to be explored about zoonotic TBDs in the region. The application of various molecular techniques has advanced the knowledge of tick-borne pathogens in Southeast Asian countries in the last two decades. Several tick-borne pathogens have been identified and characterized by molecular analysis. This chapter aims to provide what is already established about TBDs in Southeast Asia and identify the gaps that will direct future investigations. Starting with an overview of TBDs, the advancement of tick-borne pathogen research in Southeast Asia will then be reviewed. Early studies in the region employing conventional techniques will be described, yet the focus will be on the significant research findings that used various molecular tools.