Hamatopeduncularia was erected with Hamatopeduncularis arii as the type species. This genus comprises monogenoidean species mostly found as ectoparasites of marine catfishes belonging to the Ariidae. There is a significant taxonomic ambiguity among Hamatopeduncularia species due to their morphological similarity, but so far only a few morphological studies have succeeded in addressing interspecific variation and relationships. Moreover, little molecular data is available for this genus. A multidisciplinary, integrated study consisting of morphological, morphometric and molecular analyses was conducted on different species of Hamatopeduncularia recovered from the gills of two marine catfishes, Arius jella Day and Plicofollis dussumieri (Valenciennes). Five species of Hamatopeduncularia, two of which represent new species, were investigated: H. arii, H. elongatum, H. thalassini, H. madhaviae sp. nov. and H. bifida sp. nov. Phylogenetic analysis was performed using the 18S rDNA sequence as a molecular marker. The most important results of the present work are: (1) the multidisciplinary description of two novel species; (2) the multidisciplinary redescription of two species and of the type species of the genus; (3) the first molecular characterisation of 18S rDNA sequences of five species of genus Hamatopeduncularia; and (4) molecular support for the monophyly of the genus. http://zoobank.org/urn:lsid:zoobank.org:act:1333F4CC-E497-4D0A-AD7D-276D44AE6413 http://zoobank.org/urn:lsid:zoobank.org:act:43D18F75-6F4A-4F9B-8C00-6234E5BA6526