Hydroides brachyacantha Rioja, 1941, an important fouling serpulid species originally described from Mazatlán (Southern Gulf of California, Mexico) and Acapulco (southern Mexican Pacific), has been reported from the Mexican Pacific and numerous tropical and subtropical localities. However, a recent description of H. amri Sun, Wong, ten Hove, Hutchings, Williamson & Kupriyanova, 2015 from Australia, which was historically misidentified as H. brachyacantha, suggested that the widespread ‘H. brachyacantha’ is indeed a species complex. To test the status of H. amri, we conducted phylogenetic analyses based on a combined dataset of 18S rRNA, internal transcribed spacer-2, and cytochrome b sequences of H. brachyacantha from the type locality in Mexico with those of H. amri from Australia. Our molecular data supported the morphology-based hypothesis of H. amri and H. brachyacantha sensu stricto as two distinct species. Furthermore, H. amri comprises two non-sister well-supported clades. Hydroides amri thus comprises what we consider two cryptic species with long-term isolation. Here we describe the genetic lineage in South Australia as Hydroides nikae, sp. nov. Given the absence of a holotype of H. brachyacantha, we designate a neotype collected from the type locality (Mazatlán, Mexico). This study calls for a worldwide revision of the H. brachyacantha-complex.