Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member Compsopogon caeruleus was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater Compsopogon caeruleus. It was inferred that the freshwater members of Rhodophyta occurred through diverse origins based on evidence of genome size, GC-content, phylogenomic analysis and divergence time estimation. The freshwater species Compsopogon caeruleus and Hildenbrandia rivularis originated and evolved independently at the inland water, whereas the Bangia atropurpurea, Batrachospermum arcuatum and Thorea hispida are derived from the marine relatives. The typical freshwater representatives Thoreales and Batrachospermales are probably derived from the marine relative Palmaria palmata at approximately 415–484 MYA. The origin and evolutionary history of freshwater Rhodophyta needs to be testified with more organelle genome sequences and wider global sampling.

Batrachospermum is a widely distributed genus in China. Nonetheless, many taxa recorded previously have no molecular data. In this study, a new species of Batrachospermum called Batrachospermum qujingense is described and illustrated from Qujing, Yunnan, Southwest China, based on morphological observations and a phylogenetic analysis. This species is distinguished morphologically from other species by dioecious thalli, straight carpogonial branches with 7–9 cells and stalked angled obovoid or inflated-clavate trichogynes. In addition, a phylogenetic analysis of the molecular data from the rbcL, COI-5P, and psbA genes indicated separation between the new species proposed in this study and other species in the genus Batrachospermum (4.0–5.3% for rbcL, 7.7%–10.6% for COI-5P, and 2.2–3.2% for psbA ). This is the first species of Batrachospermum reported in Yunnan and the third species of Batrachospermum with molecular data in China. The description of the new species and geographical distribution expands the diversity of freshwater red algae in China.

Caloglossa (Ceramiales, Rhodophyta) is a globally distributed euryhaline red macroalgal genus. However, only a few Caloglossa species have been documented in permanent freshwater habitats. Here, a new Caloglossa species, Caloglossa fonticola sp. nov., is described and illustrated from an underground spring in Bama County, Guangxi, China, based on morphological observations and molecular phylogenetic analysis. The new species is morphologically distinguishable from other species in the genus by a unique combination of character states, including thallus internodal blades linear, hardly or slightly constricted at nodes, adventitious branches and endogenous branches both absent, and unicellular rhizoids forming from clusters of wing cells arising from the first three axial cells of the main axis and lateral axis. Phylogenetic analysis based on rbcL and LSU rRNA DNA sequences indicated that Caloglossa fonticola was nested in a well-supported clade with Caloglossa bengalensis (Bootstrap supports for ML/posterior probabilities for BI: rbcL-98/1.00, LSU-100/1.00), with high sequence divergence between these two species (8.2–8.4% for rbcL and 3.2% for LSU), supporting its specific status. This is the first species of the genus Caloglossa reported in spring water habitats. The description of C. fonticola expands the known diversity of Caloglossa.

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Kumanoa belonging to the order Batrachospermales is the most species-rich and widely distributed genus of freshwater red algae in China. In this study, a new Kumanoa species is described and illustrated from Baiyun Mountain, Guangdong, China, based on morphological observations and phylogenetic analysis. Kumanoa baiyunensis sp. nov is morphologically distinguished from other species by presenting a small habit (0.5–1 cm tall) with abundant branching in upper part of the thallus; carposporophytes spherical and one per whorl; club-shaped trichogynes with distinct stalk; spermatangia sparse and single-grown, terminal on primary fascicles. Phylogenetic analysis based on the concatenated rbcL+COI-5P+UPA alignment places Kumanoa baiyunensis in a well-supported clade (98/0.96, bootstrap proportion/posterior probability) sister to K. faroensis (from USA) and K. spermatiophora (from Hawaii) with high divergence (rbcL: 4.9%–5.0%, COI-5P: 10.1%–10.5%, UPA: 2.3%). In addition, K. baiyunensis can be easily distinguished from ten Kumanoa species reported in China through morphological features such as small thallus size, abundant branching in upper parts of the thallus, and spermatangia sparse, single-grown, and terminal on primary fascicles. The description of this new species expands the diversity of genus Kumanoa in the world.