Abstract The Rhynie chert (Aberdeenshire, Scotland, UK) plant Horneophyton lignieri is likely one of the most studied elements of Lower Devonian floras considering both macro and microremains. Intriguingly, while larger plant fragments are exceptionally fossilized, in situ spores are not necessarily well-preserved in the chert: they are dark brown and intensively torn overall. However, spore masses are often dominated by single spores, which can be taxonomically attributed. Mainly, Horneophyton spores have been described as belonging to Apiculiretusispora type and Emphanisporites cf. decoratus, this last one being currently accepted in general. Here, we document new Horneophyton spore morphologies, that are sometimes quite different. Such morphologies include, but are not restricted to, Ambitisporites, Dibolisporites or Retusotriletes. All these observed spore morphotypes belong to the same palaeobiological entity, as they have been found in the same parent plant. These findings show that the sporangia of a same plant species may deliver diverse taxa of coeval isolated spores. But most importantly, if these spores are found in sediments, they would most probably be identified as different dispersed miospore taxa. This highlights that caution is needed when comparing plant diversity with the dispersed spore fossil record. Moreover, we confirm the presence of Emphanisporites decoratus inside most of the sporangia of Horneophyton lignieri, and its high morphological variability. We further discuss the role of the different states of maturation and preservation, as well as taphonomy-induced features, on observed spore diversity.