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The lichenized green microalga <i>Trebouxia lynnae</i> Barreno has been recently described and is considered a model organism for studying lichen chlorobionts. Its cellular ultrastructure has already been studied in detail by light, electron, and confocal microscopy, and its nuclear, chloroplast and mitochondrial genomes have been sequenced and annotated. Here, we investigated in detail the ultrastructure of in vitro grown cultures of <i>T. lynnae</i> observed by Low Temperature Scanning Electron Microscopy (LTSEM) applying a protocol with minimum intervention over the biological samples. This methodology allowed for the discovery of ultrastructural features previously unseen in <i>Trebouxiophyceae</i> microalgae. In addition, original Transmission Electron Microscopy (TEM) images of <i>T. lynnae</i> were reinterpreted based on the new information provided by LTSEM. The nucleolar vacuole, dictyosomes, and endoplasmic reticulum were investigated and reported for the first time in <i>T. lynnae</i> and most likely in other <i>Trebouxia</i> lineages.