Here we investigate megaspores from 10 Triassic-Jurassic localities of southern Sweden and Bornholm, Denmark, based on collections housed in the Swedish Museum of Natural History. We identify and describe 19 megaspore taxa belonging to three stratigraphically constrained assemblages, representing the Rhaetian, Hettangian and Pliensbachian, respectively. Megaspores are abundant and diverse (12 taxa) in the Rhaetian assemblage. Diversity markedly decreases across the Triassic-Jurassic boundary (TJB), with species richness reducing from 12 to two taxa. The Hettangian assemblage is well-preserved but depauperate, and is overwhelmingly dominated by Nathorstisporites hopliticus. A subsequent recovery of lycopsid diversity followed, recorded by an increase in richness to six taxa in the Pliensbachian assemblage. The disappearance of the hygrophilous and diverse heterosporous lycophyte communities across the TJB, suggests a shift to drier conditions in the earliest Jurassic. This is supported by lithological changes from coal-forming environments in the Rhaetian to sandstone-dominated fluvial-estuarine facies in the Hettangian. Throughout this study, we analysed the megaspores using fluorescence microscopy, which revealed detailed morphological features on specimens that were otherwise opaque under visible light. This non-destructive technique is particularly useful for examining opaque megaspores embedded in permanent mounting media, such as epoxy resin, and may provide new insights into historical megaspore collections elsewhere.