Rhipicephalus haemaphysaloides is endemic in South and Southeast Asia, and it is known to parasitise domestic animals such as cattle, horses, sheep, and dogs. Despite infestation on multiple hosts, little attention has been paid to its morphological and molecular variation. The present study describes local morphological abnormalities for the first time in R. haemaphysaloides from Malaysia, and highlights the presence of three cytochrome c oxidase subunit I (COI) operational taxonomic units with 0.46-9.81% distances within the so-called R. haemaphysaloides in Malaysia, Thailand, and Pakistan.