Ribosomal RNA (rRNA) constitutes a large proportion of total RNA, often making it necessary to deplete rRNA to enrich other RNA species for downstream applications. Ribodepletion is particularly challenging in Euglena gracilis, as its large subunit (LSU) rRNA is inherently fragmented into 14 stable pieces, rendering standard depletion methods ineffective. To address this limitation, we developed a targeted depletion strategy employing sequence-specific oligonucleotides and streptavidin beads to selectively remove rRNA while preserving other RNA species. Furthermore, the modular design of our oligonucleotide probe system facilitates straightforward adaptation to other euglenids and euglenozoans, thereby advancing transcriptomic research in this evolutionarily significant protist group.