The Cordobés Formation and the basal section of the La Paloma Formation, from the borehole La Paloma a-186 and the Devonian outcrops of the Chacoparaná Basin, in Uruguay, yielded diverse and well-preserved marine and terrestrial palynomorphs. The palynological assemblages show a clear predominance of marine palynomorphs, with 75 species composed mainly of acritarchs and chlorophytes with subordinated chitinozoans and scolecodonts, and 48 terrestrial palynomorphs species composed mainly of trilete spores and subordinated cryptospores, non-marine palynomorphs and phytodebris. The palynological assemblages enable the constraining of the age of the lower and middle parts of the Cordobés Formation to the late Pragian—early Emsian, while the upper part of this unit and the basal part of the La Paloma Formation can be assigned to the early Emsian. The relative palynomorph abundances throughout the studied samples support the palaeoenvironment interpretation, based on sedimentology and depositional sequences studies, that indicates the transition from transgressive deposits in a restricted platform of the Cordobés Formation to wave-dominated shelf deposits of the La Paloma Formation. The Gondwanan affinities of the Devonian of Uruguay are confirmed by the presence of marine and terrestrial palynomorph taxa restricted to this palaeocontinent. A new trilete spore species, Distaverrusporites steemansii, is described and a new informal acritarch group, the Evittia sommeri-Evittia geometrica Group, is proposed.