Morphological plasticity stands out as a primary source of difficulty in sponge taxonomy. Ectyoplasia ferox is an abundant sponge in tropical marine ecosystems, known for producing a diverse array of bioactive compounds with allelopathic, antipredation, and pharmacological properties. However, the taxonomy of E. ferox is complex, as specimens with and without clavulate acanthostyles have been observed in both the Caribbean and Brazil. To assess the phylogeny of Ectyoplasia and the phylogenetic signal of the clavulate acanthostyles in E. ferox, we describe and compare the external morphology, skeletal organization, spicule composition, and sequences of the nuclear gene 28S rRNA (regions D3–D5) and the mitochondrial gene cox-1 in Caribbean and Brazilian specimens of E. ferox, both with and without clavulate acanthostyles. Phylogenetic analyses of both genes supported that all specimens examined belong to the same species, and therefore the presence/absence of clavulate acanthostyles lacks phylogenetic signal in this species. Moreover, the 28S tree strongly supported the non-monophyly of the genus Ectyoplasia, because E. ferox and the type species of the genus, Ectyoplasia tabula, fell into widely separate clades. Morphological evidences also support this non-monophyly, as E. ferox exhibits undifferentiated axial and extra-axial skeletons without ectosomal specialization, which are inconsistent with the current diagnosis of the genus. The placement of E. ferox in the Raspailiidae was supported by the phylogenetic analysis, despite the absence of a typical “raspailiid” ectosomal skeleton and the lack of acanthostyles in some specimens. Our study, like many others, highlights the need to integrate both morphological and molecular data from various specimens across different localities for sponge species delimitation and phylogeny.