Two new species of two genera of the order Diphyllidea van Beneden in Carus, 1863, Halysioncum Caira, Marques, Jensen, Kuchta et Ivanov, 2013 and Echinobothrium van Beneden, 1849 sensu stricto are described from Aetomylaeus cf. nichofii (Bloch et Schneider) off the Iranian coast of the Persian Gulf. Halysioncum kishiense sp. n. differs from all other congeners in the number of apical hooks with the exception of H. hoffmanorum (Tyler, 2001) and H. pigmentatum (Ostrowski de Núñez, 1971). Halysioncum kishiense sp. n. can be easily differentiated from H. hoffmanorum and H. pigmentatum by the number of hooklets and testis numbers. Echinobothrium parsadrayaiense sp. n. is differentiated from all its congeners except for E. acanthinophyllum Rees, 1961 by its hook formula. The number of spines per column on the cephalic peduncle, the number of testes and possession of a thick-walled rather than thin-walled vagina distinguish E. parsadrayaiense sp. n. from E. acanthinophyllum. To date, with these two new species, five species of Diphyllidea have been reported from the Persian Gulf.