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Abstract Over the last 2 decades, routine collections in the Hawaiian Archipelago have expanded to mesophotic reefs, leading to the discovery of a new red algal genus and species, here described asAnunuuluaehu liulagen. et sp. nov. This study provides a detailed genus and species description and characterizes chloroplast and mitochondrial organellar genomes. The new genus,Anunuuluaehu, shares many characteristics with the family Phyllophoraceae and shows close similarities toArchestennogrammaandStenogramma, including habit morphology, nemathecia forming proliferations at the outer cortex with terminal chains of tetrasporangia, and carposporophytes with multi‐layered pericarps. The single species in this genus exhibits distinctive features within the Phyllophoraceae: the presence of single‐layer construction of large medullary cells and the development of long, tubular gonimoblastic filaments. Multi‐gene phylogenetic analyses confirmed it as a unique, monophyletic lineage within the family. Cis‐splicing genes, interrupted by intron‐encoded proteins within group II introns, are present in both the chloroplast and mitochondrial genomes ofA. liula. Notably, a specific region of thecoxI group II intron exhibits similarity to fungal introns.Anunuuluaehu liulais presumed to be endemic to the Hawaiian Archipelago and thus far is known to live solely at mesophotic depths from Hōlanikū to Kaho‘olawe ranging from 54 to 201 m, which is the deepest collection record of any representative in the family. Overall, this study enhances our understanding of the genomic and taxonomic complexities of red algae in mesophotic habitats, emphasizing the significance of continued research in this area to uncover further insights into evolutionary processes and biogeographic patterns.