Marine protists are important in all marine ecosystems, but many are not culturable and therefore difficult to study. The increasing development of single-cell techniques is allowing for more marine protists to be studied, but many single-cell protocols are only optimized for model organisms and do not perform well with marine plankton. The SMART-seq v4 manual specifically states that cells entering the pipeline should be washed and resuspended in cell culture-grade PBS, but most marine protists do not tolerate PBS. Additionally, many marine protists have mineral skeletons, the components of which may interfere with the chemistry of the SMART-seq kit. Calcium and Strontium both dissolve to form divalent cations which could saturate the kit's RNase inhibitor. When we synthesized cDNA directly from acantharians (SrSO4 skeletons) without first extracting RNA, the cDNA was highly degraded with a 300 bp average fragment length. Therefore, it is desirable to perform RNA extractions from single marine protists before cDNA synthesis and amplification, but the amount of RNA in single marine protists is too low to be extracted with column-based kits (even the MN Nucleospin RNA XS kit suggested in the SMART-seq manual). To overcome these problems, we developed a column-free method for extracting RNA from single marine protists by making use of Agencourt RNAClean XP magnetic beads. When this protocol is followed, the synthesized cDNA is higher quality with a 2,000 bp average fragment length.