Zygosporium Mont. (Zygosporiaceae, Xylariales, Sordariomycetes) is known to have saprophytic or parasitic relationship with various modern angiosperms. Fossil record of such an interaction is unknown till date. Here, we report in situ occurrence of asexual morphs of two fossil species of Zygosporium from the Neogene Siwalik sedimentary strata of eastern Himalaya for the first time. Z. palaeotuberculatum sp. nov. is found to be interacting with leaves cf. Woodfordia sp. Khan et al. (Lythraceae) and Glochidion palaeogamblei Khan and Bera (Euphorbiaceae) from the lower Siwalik strata of Darjeeling (middle Miocene to late Miocene) and middle Siwalik strata of Arunachal sub-Himalaya (Pliocene) respectively, whereas, Z. miochinensis sp. nov. is found on the leaf cuticle of Terminalia panandhroensis Lakhanpal and Guleria (Combretaceae) from the Formation II (Pliocene) strata of Bhutan. These fungal morphotypes possibly developed in a tropical evergreen to deciduous forest under warm, moist environmental condition in the eastern Himalaya during deposition.