Myliocotyle borneoensis sp. n. and M. multicrista sp. n. (Monocotylidae: Heterocotylinae) are described from the gills of the mottled eagle ray, Aetomylaeus maculatus (Gray), and the banded eagle ray A. nichofii (Bloch et Schneider) (Myliobatidae), respectively, collected from the northern coast of Malaysian Borneo. These are the first monogeneans to be described on elasmobranchs from Borneo. The formerly monotypic Myliocotyle (for M. pteromylaei) was distinguished from other monocotylids by the distribution and morphology of the eight sclerotised dorsal haptoral accessory structures and the morphology of the male copulatory organ. However, we have determined that M. pteromylaei has ten structures on the dorsal surface of the haptor. Myliocotyle borneoensis is distinguished from M. pteromylaei by the morphology of the male copulatory organ and its accessory piece. Myliocotyle multicrista has 12 sclerotised dorsal haptoral accessory structures and a male copulatory organ with two accessory pieces. Additional sclerotised ridges across the ventral surfaces of each loculus (except the posterior-most pair) are also present in M. multicrista. The diagnosis for Myliocotyle is revised given our discovery of additional dorsal haptoral accessory structures in the type species and to accommodate other new characters of the two new species. Anterior secretions of Myliocotyle are discussed.