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Abstract Marine protists are globally distributed and sensitive to environmental conditions, which makes them a focal group when studying the effects of climate change on biodiversity and ocean health. However, they are a highly diverse group with varying evolutionary histories and morphologies and widely variable preservation potential in the fossil record. Thus, their past diversity and composition are poorly known. Paleogenetics, which relies, among other approaches, on DNA metabarcoding of sedimentary ancient DNA (sedaDNA), provides a promising avenue to explore the past history and responses of marine protists to global change. Choosing the right marker for sedaDNA studies is critical, striking a balance between marker length and taxonomic resolution. While marker guides exist for modern environmental DNA surveys, a thorough assessment of existing short markers for sedaDNA studies targeting protists is lacking. In this study, we report on a comparison of in silico PCR for eight short 18S rDNA markers, including one from the Tara Oceans initiative and a longer marker commonly used in modern marine eDNA studies. We analyze their taxonomic coverage and resolution, taxonomic overlap and uniqueness between markers, co‐amplification of non‐protist taxa, and amplicon size differences across taxonomic groups. Additionally, we provide a detailed analysis of diatoms, dinoflagellates, haptophytes, and chlorophytes. Our study is aimed at supporting project‐specific marker choices for characterizing protist composition and diversity. While we focus on marine protists, our results are applicable to other aquatic and terrestrial environments.