Palaeonitella cranii is a charophyte alga (Charophyceae) from the Lower Devonian Rhynie chert of Scotland that consists of an axis of alternating internodes and nodes, with whorls of branchlets arising from the nodes. Conspicuous spherical to ovoid structures believed by most to be the bulbils of P. cranii are often found together with the axes and branchlets; however, they have so far only been insufficiently studied. Here, we revisit the bulbils, along with the rhizoids on which they were formed, based on new material from the Rhynie and Windyfield chert sites. The bulbils are up to 540 μm in diameter and occur singly or in groups on rhizoid nodes. A small node recognizable at the apical end in some specimens is evidence that the bulbils are modified branch rhizoids. There is also evidence of lower-order branch rhizoids extending from the apical node, as well as for sprouting. Palaeonitella cranii thrived in shallow pools and outflow channels of the Rhynie geothermal wetland. The bulbils might have enabled the plant to persist if photosynthesis was limited and to regenerate if the thallus was destroyed, but they might also have served as dispersal units. Other significantly inflated cells, which are not bulbils, may occur in both axes and branchlets of P. cranii, but are generally rare. Some of these cell alterations may be due to parasites. This study complements our understanding of P. cranii, the only fossil charophyte known from both above- and below-ground parts of the thallus, and from reproductive structures.