Investigations on myxozoan parasites of fish from Chongqing in China, revealed two Myxidium cuneiforme-like myxosporeans infecting the gallbladder of Cyprinus carpio carpio and Carassius auratus. We researched their myxospore morphology, and analyzed their genetic similarity and phylogenic relationships to other myxozoans based on small subunit ribosomal DNA (18S rDNA) sequences. Although both parasites recovered were morphologically similar, the myxosporean isolated from C. auratus was consistent in morphology to Myxidium cuneiforme, which was described from this host species. The parasite isolated from C. c. carpio had overlapping myxospore dimensions to M. cuneiforme, but on average, the polar capsules were not as long. More importantly, this parasite was genetically distinct from M. cuneiforme with 96.3% and 96.5% similarity in two sequences of 18S rDNA, and we propose the name Myxidium pseudocuneiforme n. sp. for this myxozoan from common carp. Its mature myxospores are ellipsoidal and asymmetric with pointed ends in valvular view, arc-shaped or fusiform in sutural view. The pyriform polar capsules are equal in size, and polar filament with 5–6 coils. This study highlights that molecular characteristics and host specificity are indispensable for myxozoan species identification when presented with the taxonomic dilemma of whether we are observing one species that exhibits slight morphological differences or multiple, but similar, species in different hosts.