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Background  The morphotaxonomy of  Rhipicephalus microplus  complex has been challenged in the last few years and prompted many biologists to adopt a DNA-based method for distinguishing the members of this group. In the present study, we used a mitochondrial DNA analysis to characterise the genetic assemblages, population structure and dispersal pattern of  R. microplus  from Southeast Asia, the region where the species originated.    Methods  A phylogeographic analysis inferred from the 16S rRNA and cytochrome oxidase subunit I (COI) genes was performed with five populations of  R. microplus  collected from cattle in Malaysia. Malaysian  R. microplus  sequences were compared with existing COI and 16S rRNA haplotypes reported globally in NCBI GenBank.    Results  A total of seven and 12 unique haplotypes were recovered by the 16S rRNA and COI genes, respectively. The concatenated sequences of both 16S rRNA and COI revealed 18 haplotypes. Haplotype network and phylogenetic analyses based on COI+16S rRNA sequences revealed four genetically divergent groups among Malaysian  R. microplus . The significantly low genetic differentiation and high gene flow among Malaysian  R. microplus  populations supports the occurrence of genetic admixture. In a broader context, the 16S rRNA phylogenetic tree assigned all isolates of Malaysian  R. microplus  into the previously described African/the Americas assemblage. However, the COI phylogenetic tree provides higher resolution of  R. microplus  with the identification of three main assemblages: clade A sensu Burger  et al.  (2014) comprises ticks from Southeast Asia, the Americas and China; clade B sensu Burger  et al.  (2014) is restricted to ticks that originated from China; and clade C sensu Low  et al.  (2015) is a new genetic assemblage discovered in this study comprising ticks from India and Malaysia.    Conclusions  We conclude that the  R. microplus  complex consisting of at least five taxa:  R. australis ,  R. annulatus ,  R. microplus  clade A sensu Burger  et al.  (2014),  R. microplus  clade B sensu Burger  et al.  (2014) and the new taxon,  R. microplus  clade C sensu Low  et al.  (2015). The use of COI as the standard genetic marker in discerning the genetic assemblages of  R. microplus  from a broad range of biogeographical regions is proposed.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-015-0956-5) contains supplementary material, which is available to authorized users.

parasites and vectors

Molecular characterisation of the tick Rhipicephalus microplus in Malaysia: new insights into the cryptic diversity and distinct genetic assemblages throughout the world