An enigmatic, yellowish-brown, variably branched organic-walled microfossil (palynomorph) marks the Late Glacial Maximum of Upper Pleistocene sediments in the Marmara Sea. This taxon, previously called a Multiplicisphaeridium-type acritarch, a putative algal cyst, or a possible chytrid fungus, virtually disappears at the end of the Ponto-Caspian lacustrine phase, making it a valuable marker for regional ecostratigraphic correlation. However, uncertainty surrounding its biological affinity limits interpretations of its taxonomy, palaeoecology, evolutionary history, and broader geographic significance. We document the morphology and variability of well-preserved cf. Multiplicisphaeridium specimens from Marmara and Black Sea sediment cores using interference light microscopy and scanning electron microscopy. Detailed morphological comparisons with visually similar acritarchs, chytrids, and dinoflagellates indicate a plausible, though non-definitive, affinity with chytrid fungi and exclude pre-Quaternary sedimentary reworking. Compositional analyses using attenuated total reflection Fourier transform infrared microspectroscopy reveal a close biomacromolecular match between cf. Multiplicisphaeridium and co-occurring chytrid sporangia, including evidence of wall melanisation potentially characteristic of chytrids but distinct from other fungal clades. Additional comparative analyses of sporangia from extant marine Rhizophydium further contextualize chytrid wall taphonomy. The combined morphological and molecular evidence favours a chytrid-like affinity and demonstrates distinction from true Multiplicisphaeridium acritarchs, but does not justify assignment to a known chytrid lineage (extant Arkaya is identified as a potential close analogue). We therefore erect a new genus and species within the Acritarcha, Palaeoarkaya similis gen. et sp. nov., and discuss its potential significance in low-salinity glacial palaeoenvironments. This integrative morpho-molecular approach confirms earlier evidence of possible fungal affinity among acritarchs.