A new lecanicephalidean species of Aberrapex Jensen, 2001 is described from the blue-spotted fantail ray Taeniura lymma (Forsskål) collected off the eastern coast of Sabah in Malaysian Borneo. This is the first record of a lecanicephalidean tapeworm from the island of Borneo and the first record of Aberrapex from this host species. A. manjajiae n. sp. is easily distinguished from its two congeners, A. senticosus Jensen, 2001 and A. arrhynchum (Brooks, Mayes & Thorson, 1981) Jensen, 2001, based on its overall smaller size (928–1,971 vs 1,485–6,333 and up to 3,350μm long, respectively) and fewer testes (10–19 vs 20–40 and 18–25, respectively). In addition, A. manjajiae n. sp. is readily distinguished from A. senticosus based on a more anteriorly positioned genital pore (76–85 vs 52–72% of proglottid length from posterior end) and its distal bothridial microthrix pattern. A. manjajiae n. sp. can be further distinguished from A. arrhynchum based on its smaller scolex (82–101 × 119–164 vs 177–186 × 233–326μm). The host distribution of Aberrapex is expanded from the Myliobatidae to include the Dasyatidae.