We describe Schikhobalotrema huffmani n. sp. from Tylosurus crocodilus (Péron and Leseur) (Belonidae) collected off Lizard Island, Great Barrier Reef, Queensland, Australia and Tylosurus gavialoides (Castelnau) collected from Moreton Bay, Queensland. Schikhobalotrema huffmani n. sp., along with Schikhobalotrema ablennis (Abdul-Salam and Khalil, 1987) Madhavi, 2005, Schikhobalotrema acutum (Linton, 1910) Skrjabin and Guschanskaja, 1955 and Schikhobalotrema adacutum (Manter, 1937) Skrjabin and Guschanskaja, 1955 are distinguished from all other species of Schikhobalotrema Skrjabin and Guschanskaja, 1955 in having ventral suckers which bear lateral lobes and have longitudinal apertures. Schikhobalotrema huffmani n. sp. differs from S. ablennis in having an obvious post-vitelline region and a longer forebody. From S. acutum, S. huffmani n. sp. differs in having a prostatic bulb smaller than the pharynx and more anterior testis. From S. adacutum, S. huffmani n. sp. differs in having more prominent ventral sucker lobes, a conspicuous prostatic bulb and a longer forebody. We also report the first Australian record of Haplosplanchnus pachysomus (Eysenhardt, 1829) Looss, 1902, from Mugil cephalus Linnaeus (Mugilidae) collected in Moreton Bay. Molecular sequence data (ITS2, 18S and 28S rDNA) were generated for Schikhobalotrema huffmani n. sp., H. pachysomus and archived specimens of Hymenocotta mulli Manter, 1961. The new 18S and 28S molecular data were combined with published data of five other haplosplanchnid taxa to expand the phylogeny for the Haplosplanchnata. Bayesian inference and Maximum Likelihood analyses recovered identical tree topology and demonstrated the Haplosplanchnata as a well-supported monophyletic group. However, relationships at and below the subfamily level remain poorly resolved.