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The first Holocene record of the freshwater ascomycete Megalohypha aqua-dulces from the sediment core Kongor (NE Iran) is presented here. Based on the similarity of the spore morphology with the fossil form genus Fusiformisporites, we establish a link between extant and fossil taxa. Comparative analysis of morphological characteristics of fossil spores of Fusiformisporites indicates that several different fungal groups might be included in this form genus. At least five species of Fusiformisporites share similar morphology with spores of Megalohypha aqua-dulces: Fusiformisporites annafrancescae, Fusiformisporites crabbii, Fusiformisporites keralensis, Fusiformisporites paucistriatus, and Fusiformisporites pseudocrabbii. Based on Fusiformisporites, the evolution of Megalohypha aqua-dulces can be traced to the late Cretaceous, corresponding with diversification of the flowering plants and pointing to a co-evolution of both groups. Megalohypha aqua-dulces has a tropical to subtropical distribution but also occurs in the semi-arid steppe environments of Kongor together with other freshwater fungal genera such as Xylomyces, Dictyosporium, and Sporoschisma, which spores we describe here. The ecological requirements of Megalohypha indicate that its spores can be used for the palaeoecological sign of dead submerged wood as well as of tropical to subtropical conditions. (c) 2017 Elsevier B.V. All rights reserved.