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Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we optimized a microarray single-cell sequencing (MASC-seq) technology that generates microscope images of cells in parallel with capturing their transcriptomes. We tested the method on three species representing important plankton groups with different cell structures, the ciliateTetrahymena thermophila, the diatomPhaeodactylum tricornutumand the dinoflagellateHeterocapsasp.. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating “microbial dark matter”, although further optimizations are necessary to increase the signal-to-noise ratio.