From 1999 through 2012, a total of 541 individual rodents (jerboas of the family Dipodidae) were collected from several habitat types, primarily from the Gobi region of Mongolia, and were examined for helminth and protistan parasites. Of those rodents, 25 were identified as Pygeretmus pumilio Kerr, 1792 (Rodentia: Dipodidae), whereas 516 were other species of jerboa from the provinces of Dornogobi, Dundgobi, Omnogobi, Ovorhangai, Bayanhongor, Gobi Altai, and Hovd. During our field work, we collected several cestodes; some of which represented undescribed species, and these new species occurred in 40% of P. pumilio from four separate collecting localities. We designate this new species as Catenotaenia tuyae n. sp. (Cyclophyllidea: Catenotaeniidae), which is characterized by having relatively long and narrow gravid proglottids and an ovary in mature segments that is located antiporally in the anterior portion of the mature proglottids. In addition, the position and the ratio of the genital pore toward the anterior end of the proglottids are unique and the ovary is elongate, being confined to the antiporal part of the mature proglottid. These morphological features serve to differentiate Catenotaenia tuyae from all other species in the genus included in the phylogenetic analysis and are supported by molecular phylogenetic evidence using the 28S ribosomal RNA gene. The intensity of C. tuyae infection in Pygeretmus ranged from 1 to 3 individual cestodes per infected host.