Three new Rhinebothrium Linton, 1890 species, R. kinabatanganensis n. sp., R. megacanthophallus n. sp., and R. abaiensis n. sp., collected from the spiral intestines of 6 freshwater whiprays (Himantura chaophraya, Dasyatidae) in the Kinabatangan River, Malaysian Borneo, are described. This is the first record of cestodes from the Kinabatangan River and from H. chaophraya. The new Rhinebothrium species are differentiated from the 34 valid Rhinebothrium species in addition to 2 species, Echeneibothrium hui Tseng, 1933 and E. oligotesticularis Subramaniam, 1940 that are herein transferred to Rhinebothrium. Each of the new species was examined with light and scanning electron microscopy. Two of the new species possess cilia on their bothridia, which have not previously been reported for members of this genus.