The biota of the brackish-water Lake Pannon in the Pannonian Basin is characterised by remarkable endemism due to the isolated evolution of the lake for 8 myr after the last Miocene marine connection ceased (∼11.6 Ma). A conspicuous feature of this endemism is the large, probably ecophenotypic variation in the morphology of brackish-water dinoflagellate cysts that challenges taxonomy and complicates biostratigraphical and ecological interpretations. We conclude that a widely debated Lake Pannon genus, Pontiadinium, includes several proximate dinoflagellate cyst species with prominent apical and antapical protuberances, and we show how the genus differs from the morphologically similar gonyaulacacean cyst genera Impagidinium, Leptodinium, Cribroperidinium and Komewuia. The generic description of Pontiadinium is emended together with the species descriptions of Pontiadinium inequicornutum, Pontiadinium obesum and Pontiadinium pecsvaradanesis. A new species is described as Pontiadinium szentaiae sp. nov. from Našice (northern Croatia) that is characterised by unique trabeculate sutural septa formed from a beaded tegillum supported by columellae or rod-like luxuriae. The dinoflagellate cyst assemblages of the long-lived brackish-water Lake Pannon clearly demonstrate that dinoflagellate cysts in low-salinity, isolated epicontinental seas display greater morphological plasticity than their normal-marine relatives. The development of an antapical horn appears to be a previously undocumented example of phenotypic morphological features that developed in response to subnormal salinities within at least two dinoflagellate cyst genera endemic to Lake Pannon and the Post-Paratethyan seas of the Ponto-Caspian realm. This ecophenotypic variation resulted in a higher level of morphological adaptation, leading to the evolutionary development of new dinoflagellate cyst species and genera.