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The classification of coralline algae commonly relies on the morphology of cells and reproductive structures, along with thallus organization, observed through Scanning Electron Microscopy (SEM). Nevertheless, species identification based on morphology often leads to uncertainty, due to their general plasticity. Evolutionary and environmental studies featured coralline algae for their ecological significance in both recent and past Oceans and need to rely on robust taxonomy. Research efforts towards new putative diagnostic tools have recently been focused on cell wall ultrastructure. In this work, we explored a new classification tool for coralline algae, using fine-tuning pretrained Convolutional Neural Networks (CNNs) on SEM images paired to morphological categories, including cell wall ultrastructure. We considered four common Mediterranean species, classified at genus and at the species level (Lithothamnion corallioides, Mesophyllum philippii, Lithophyllum racemus, Lithophyllum pseudoracemus). Our model produced promising results in terms of image classification accuracy given the constraint of a limited dataset and was tested for the identification of two ambiguous samples referred to as L. cf. racemus. Overall, explanatory image analyses suggest a high diagnostic value of calcification patterns, which significantly contributed to class predictions. Thus, CNNs proved to be a valid support to the morphological approach to taxonomy in coralline algae.