Samples from outcrops of the Miocene Solimões and Barreiras formations from the central and coastal Amazon regions of Brazil were analyzed palynologically. Assemblages of fossil fungi were identified, and are described herein, and their relevance to paleoenvironmental and paleoclimatic studies in tropical regions discussed. The fungal assemblage comprises four spore groups, 19 species belonging to 12 genera. Additionally, two new species are proposed. The samples from the Solimões Formation contain the following taxa: Mediaverrunites elsikii, Mediaverrunites mulleri, Monoporisporites sp., Fusiformisporites crabbii, and Multicellites cingulatus. The presence of these suggests river channel margins colonized by freshwater vegetation, where seasonal fluctuations of water table and rainfall produce wetter substrates. The samples from the Barreiras Formation showed higher species and generic diversity than those from the Solimões Formation with Hypoxylonites minutus, Hypoxylonsporites ater, Hypoxylonites sp., the new species Inapertisporites multiporus n. sp., Pluricellaesporites regularis, Lacrimasporonites levis, Monoporisporites annulatus, Spirotremesporites simplex, Dyadosporites novus, Dyadosporites sp., and Multicellaesporites attenuates. All of these correspond to parasitic fungi from a range of from tropical wetlands. Spegazzinites sp. and Dicellaesporites aculeolatus, good indicators of marine influence and mangrove presence, were also identified in the samples from the Barreiras Formation. Furthermore, the fungal spore taxa Inapertisporites multiporus, Mediaverrunites elsikii, Mediaverrunites mulleri, Pluricellaesporites regularis, and Spirotremesporites simplex serve as stratigraphic indicators when combined with miospore index taxa such as Crassoretitriletes vanraadshooveni, Grimsdalea magnaclavata and Fenestrites longispinosus indicating a Miocene age for these sediments in the Amazon region.