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A variety of depositional environments characterise the infill of the late Permian Bowen and Galilee basins. These range from proximal fluvial-floodplain sequences and significant coal deposits through to more distal paralic and marine sections. The uppermost Permian sequence in these basins features spatiotemporal facies shifts but the regionally pervasive nature of the coal seams allows for the examination of the palaeoflora in context of changing environments through time between these bounding surfaces. The predominant flora of the southern hemisphere during the Permian was the Glossopteris-flora, dominated by its namesake along with a diverse assemblage of ferns, horsetails, lycopsids, conifers and cycads. The composition of this flora isn't entirely uniform and is subject to environmental and climatic factors. The aim of this work was to examine this variation on a basin scale across a variety of depositional environments. This should provide insight into the localised environmental controls on the palaeoflora versus significant regional patterns as well as the possibility of facies-controlled biostratigraphic taxa. Five boreholes were selected to examine the transition from a proximal terrestrial setting to a distal marine setting. The time interval selected represents a regressive phase from the last Permian marine transgression through a significant coal-bearing sequence to the Permian-Triassic Boundary. The borehole Montani 1 captures the proximal alluvial plain sequence, featuring pteridophytes and gymnosperms occupying fluvial, floodplain, and coal-bearing sequences. Non-glossopterid pollen may be indicative of transport from the hinterland or a xerophytic woodland occupying the basin margin. The borehole Glue Pot Creek 1 represents a Glossopteris-dominated upper delta plain. Three boreholes (Tambo 1-1A, Springsure 19, Taringa 7) capture a progradational deltaic sequence, which is reflected in the palynology whereby pioneer pteridophytes give way to gymnosperms upsection. The coastal pteridophytes (ferns, horsetails, cycads, lycopsids) are able to tolerate flooding and salinity changes. Unusual abundances of conifer pollen may be indicative of pollen transport, but also could represent coastal forests on more well-drained sandy soils not unlike modern coastal conifer forests.