Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for phylogenetic community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of the phycological community has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). As a proof-of-concept study, we leverage this resource to develop and apply a phylogenomic strategy to seek candidate plastid markers that best capture the identity of component species in an eDNA metabarcoding study. We ranked the core plastid genes of 107 published plastid genomes based on various sequence-derived properties and their tree distance to plastid genome phylogenies and found that the most widely used marker, rbcL, is not necessarily the optimal marker, while more informative markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of these, rpoC1, for a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for eDNA metabarcoding of the red algae.