Ticks are one of the most economically important groups of blood-sucking arthropod parasites and transmit numerous pathogens to mammals and humans. To study the phylogenetic relationships of ticks, we sequenced a 903bp-fragment of COI gene directly from PCR amplifications. With a high level of support based on posterior probability (>95%), Bayesian analysis of COI data produced highly resolved relations for three major lineages of ticks, including monophyly of the Argasidae(Ornithodoros), Prostriata (Ixodes), and Metastriata. In contrast to the existing phylogenies, our COI results showed that the Ixodes ricinus species complex is not a monophyletic group. Unlike the other molecular analyses, Amblyomma and Haemaphysalis were not placed into a sister clade and the relationship between them varied depending upon the methods used for analysis. The species of Hyalomma were not found within the clade of Rhipicephalinae. The genus Dermacentor was bascal to the subfamily Rhipicephalinae but was monophyletic. Boophilus seems to arise from Rhipicephalus. We also sequenced two fragments of 16S rDNA from 28 species of the genus Ixodes. The phylogenetic relationships derived from 16S rDNA gene agreed with that of COI. Both the Ixodes ricinus species complex and the subgenus Ixodes are not monophyletic.