Examination of spiral intestines from Himantura tutulBorsa, Durand, Shen, Arlyza, Solihin, and Berrebi, 2013 (=Himantura uarnak 3 sensu Naylor et al. [2012]), collected from Malaysian Borneo revealed the presence of a new species of tapeworm belonging to the genus Stillabothrium (Rhinebothriidea: Escherbothriidae). Stillabothrium borneoense n. sp. Herzog, Meininger, and Reyda is assigned to the genus based on its possession of a scolex with 4 bothridia divided into a distinct anterior region with facial loculi that are oriented horizontally and a distinct posterior region with facial loculi that are oriented vertically. The new species is distinguished from its congeners by features of the scolex and proglottids, including a vagina that recurves well anterior to the cirrus sac, as well as a unique locular arrangement not previously reported for members of this genus: 4 horizontally oriented loculi in the anterior region of the bothridia and 7 vertically oriented loculi in the posterior region of the bothridia. Stillabothrium borneoense n. sp. expands both known morphological variation and known host associations within the genus.