Objective To analyze the ribosomal and mitochondrial genes sequences polymorphisms of Kalicephalus indicus, and discuss their application potential as molecular markers. Methods Two wild Elaphe carinata snakes were captured in June 2016, in Zhangli Town, Changsha County, Hunan Province, and seven K. indicus adult worms were isolated from the snakes. Total DNA from the worms was extracted. The sequences of the first and second internal transcribed spacer regions 1 and 2(ITS-1 and ITS-2), 5.8S, mitochondrial cytochrome c oxidase subunit 1 (cox1), small subunit 12S of ribosomal RNA, ATP synthase subunit 6 (atp6), nicotinamide adenine dinucleotide dehydrogenase subunit 4 (nad4) of K. indicus were amplified using PCR and subjected to DNA sequencing. The sequencing results of each gene were aligned using ClustalX 1.83. A phylogenetic tree based on the mitochondrial DNA sequences cox1, 12S, atp6 and nad4 was constructed using Bayesian method, using Onchocerca volvulus as an outgroup. Intraspecific variation in these sequences among the seven K. indicus samples were analyzed. Results The size of the amplified products of ITS-1, 5.8S and ITS-2 was approximately 900 bp. The size of the amplified products of cox1, 12S, atp6 and nad4 was approximately 400, 600, 500 and 400 bp, respectively. The content of A + T of ITS-1, 5.8S and ITS-2 is 52.7%-53.7%, higher than its content of G + C (46.3%-47.4%). The content of A + T of cox1, 12S, atp6 and nad4 is 67.1%-68.9%, 76.9%-77.4%, 73.0%-75.5%, and 70.3%-73.3%, respectively, higher than their content of G + C (31.1%-32.9%, 22.6%-23.1%, 24.5%-27.0% and 26.7%-29.7%). Intraspecific variation in ITS-1, 5.8S, ITS-2, cox1, 12S, atp6 and nad4 were 0-2.5%, 0, 0-5.0%, 0-2.6%, 0-3.8%, 0.7%-8.7% and 0-11.0%, respectively. The phylogenetic tree clustered the seven K. indicus individuals into the same branch, with Ancylostoma ceylanicum being the closest species. Conclusion The ITS-2 sequence with the largest variation is expected to be an ideal molecular marker for studying the intraspecific variation of K. indicus. The degree of its intraspecific variation in mitochondrial gene sequences is as follows: cox1 < 12S < atp6 < nad4, and nad4 is an ideal mitochondrial molecular marker for studying the genetic diversity of K. indicus.