To establish a method combined morphology and molecular marker for identifying Haemaphysalis longicornis and Rhipicephalus microplus.Ticks were collected from domestic animals and wild environment in epidemic area of Hubei and Henan provinces where cases of fever with thrombocytopenia syndrome were prevalent. We classified the ticks by morphology characteristics before 12S rDNA of ticks were amplified by PCR and subsequently sequenced. Phylogenetic tree was constructed by PAUP4.0.The ticks belonged to Haemaphysalis longicornis and Rhipicephalus microplus through observation and analysed by the morphological characteristics of the ticks. 12S rDNA was cloned and sequenced while data confirmed the morphological identification of the results.The method based on morphology that combined with molecular marker seemed a good method for the identification of ticks.