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Ticks of the Boophilus subgenus, classified in the genus Rhipicephalus, are widespread in subtropical and tropical regions, but knowledge on their distribution in Asia is fragmentary. The most important representatives belong to the Rhipicephalus (Boophilus) microplus complex, which is composed of species that share many morphological similarities and are therefore difficult to distinguish. In this study, adult Rhipicephalus (Boophilus) ticks from Bangladesh, Myanmar and Pakistan were subjected to phylogenetic and Scanning Electron Microscopy (SEM) analyses. Phylogenetic analyses of cytochrome oxidase 1 (cox1), internal transcribed spacer 2 (ITS2) and 12S rRNA gene sequences confirmed that the R. microplus complex consists of at least five taxa: R. annulatus, R. australis, and R. microplus clades A-C. Ticks from Bangladesh, Myanmar and Pakistan were assigned to R. microplus clade C. SEM images revealed a wide range of variation in the morphology of the clade C adults, including morphological features previously identified as critical for distinguishing R. microplus from R. australis, which is illustrative for the complications in identifying species within the R. microplus complex using morphology only. Further morphological, genomic and crossbreeding studies are required to elucidate the species status of R. microplus clades A-C.