Abstract: Red alga species in the phylum Rhodophyta are ecologically and economically important, which are widely used as food and medicinal products because they are rich in bioactive compounds. Unfortunately, researchers often meet challenges in identifying red algal species and understanding the evolutionary relationship among them. Shooting away these limitations necessitates detailed genomic studies, including those of cellular organelles. In this study, we sequenced circular organelle genomes of three red macroalgal species, Grateloupia asiatica, Pachymeniopsis lanceolata and Polyopes affinis, yielding two complete chloroplast genomes of P. lanceolata and P. affinis and one mitochondrial genome of P. affinis. The average chloroplast and mitochondrial genome sizes were 192,724 bp and 29,699 bp, respectively, which encoded 202 and 25 proteins, respectively, on average. The short- and long-repeat sequences, gene rearrangements, the nucleotide diversity, and phylogenetic relationship among these three species were analyzed. Memo: revise conjunctions and prepositions to form a clearer list (A, B, C, and D). The 194 chloroplast and 23 mitochondrial protein-coding genes shared by the species belonging to Florideophyceae and Bangiophyceae were used to reconstruct a maximum-likelihood phylogenetic tree. In addition, we developed 15 species-specific PCR markers, five for each species, using single-nucleotide polymorphism information. Our results should aid in identifying these species and deciphering the evolutionary relationship among species in the phylum Rhodophyta.