Between brackets is the number of accepted species
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- Biota
- Kingdom Animalia
- Kingdom Archaea
- Kingdom Bacteria
- Kingdom Chromista
- Subkingdom Hacrobia
- Subkingdom Harosa
- Infrakingdom Halvaria
- Superphylum Alveolata
- Superphylum Heterokonta
- Phylum Bacillariophyta
- Phylum Bigyra
- Phylum Chrysophyta accepted as Ochrophyta
- Phylum Diatomaceae accepted as Bacillariophyta
- Phylum Eustigmatophyta accepted as Ochrophyta
- Phylum Heterokontophyta accepted as Ochrophyta
- Phylum Hyphochytriomycota accepted as Pseudofungi
- Phylum Labyrinthista accepted as Bigyra
- Phylum Ochrophyta
- Class Aurearenophyceae accepted as Phaeothamniophyceae
- Class Aurophyceae accepted as Phaeothamniophyceae
- Class Bolidophyceae
- Class Chrysomeridophyceae
- Class Chrysoparadoxophyceae
- Class Chrysophyceae
- Class Dictyochophyceae
- Class Eustigmatophyceae
- Class Hyphochytriomycetes accepted as Hyphochytrea
- Class Olisthodiscophyceae
- Class Pelagophyceae
- Class Phaeophyceae
- Order Ascoseirales
- Order Asterocladales
- Order Chordales
- Order Chordariales accepted as Ectocarpales
- Order Cutleriales accepted as Tilopteridales
- Order Desmarestiales
- Order Dictyosiphonales accepted as Ectocarpales
- Order Dictyotales
- Order Discosporangiales
- Order Durvillaeales accepted as Fucales
- Order Ectocarpales
- Family Acinetosporaceae Hamel ex J. Feldmann, 1937
- Family Acrotrichaceae accepted as Chordariaceae Greville, 1830
- Family Adenocystaceae F. Rousseau, B. de Reviers, M.-C. Leclerc, A. Asensi & R. Delépine
- Family Asperococcaceae accepted as Chordariaceae Greville, 1830
- Family Buffhamiaceae accepted as Chordariaceae Greville, 1830
- Family Chnoosporaceae Setchell & Gardner, 1925 accepted as Scytosiphonaceae Farlow, 1881
- Family Chordariaceae Greville, 1830
- Family Chordariopsidaceae Kylin, 1940 accepted as Adenocystaceae F. Rousseau, B. de Reviers, M.-C. Leclerc, A. Asensi & R. Delépine
- Family Coelocladiaceae Pedersen, 1976 accepted as Chordariaceae Greville, 1830
- Family Coilodesmaceae accepted as Chordariaceae Greville, 1830
- Family Corynophlaeaceae accepted as Chordariaceae Greville, 1830
- Family Delamareaceae accepted as Chordariaceae Greville, 1830
- Family Dictyosiphonaceae accepted as Chordariaceae Greville, 1830
- Family Ectocarpaceae C.A. Agardh, 1828
- Family Elachistaceae accepted as Chordariaceae Greville, 1830
- Family Giraudiaceae accepted as Chordariaceae Greville, 1830
- Family Leathesiaceae accepted as Chordariaceae Greville, 1830
- Family Myrionemataceae Nägeli, 1847 accepted as Chordariaceae Greville, 1830
- Family Myriotrichiaceae accepted as Chordariaceae Greville, 1830
- Family Petrospongiaceae
- Genus Petrospongium Nägeli ex Kützing, 1858
- Species Petrospongium berkeleyi (Greville) Nägeli, 1858
- Species Petrospongium kuckuckii (E. Taskin, M.J. Wynne & M. Öztürk) Cormaci & Furnari, 2012
- Species Petrospongium rugosum (Okamura) Setchell & N.L. Gardner, 1924
- Family Pilayellaceae accepted as Acinetosporaceae Hamel ex J. Feldmann, 1937
- Family Pogotrichaceae Pedersen, 1978 accepted as Acinetosporaceae Hamel ex J. Feldmann, 1937
- Family Pogotrichiaceae accepted as Acinetosporaceae Hamel ex J. Feldmann, 1937
- Family Punctariaceae accepted as Chordariaceae Greville, 1830
- Family Pylaiellaceae accepted as Acinetosporaceae Hamel ex J. Feldmann, 1937
- Family Scytosiphonaceae Farlow, 1881
- Family Sorocarpaceae accepted as Chordariaceae Greville, 1830
- Family Spermatochnaceae accepted as Chordariaceae Greville, 1830
- Family Striariaceae accepted as Chordariaceae Greville, 1830
- Order Fucales
- Order Ishigeales
- Order Laminariales
- Order Nemodermatales
- Order Onslowiales
- Order Phaeosiphoniellales
- Order Ralfsiales
- Order Scytosiphonales accepted as Ectocarpales
- Order Scytothamnales
- Order Sphacelariales
- Order Sporochnales
- Order Stschapoviales
- Order Syringodermatales
- Order Tilopteridales
- Family Archyfasmaceae Gnilovskaya, 2003 †
- Family Phaeophyceae (awaiting allocation)
- Genus Caulerpites (A.T. Brongniart) Sternberg, 1833 †
- Genus Dichothallus S.V. Naugolnykh, 2018 †
- Genus Gracilogia Ding in Ding et al., 1992 †
- Genus Houjiashania J. Liu et al., 2024 †
- Genus Jonssonia S. Lund, 1959
- Genus Miaohephyton M. Chen & Z.Z. Xiao, 1991 †
- Genus Phasganon Targioni-Tozzetti, 1826
- Genus Phasgonon Walker ex S.F. Gray, 1821
- Genus Pilonema Derbès & Solier, 1851
- Genus Porterinema Waern, 1952
- Genus Prototilopteris Funk, 1927 accepted as Zosterocarpus Bornet, 1890
- Genus Pseudobodanella J. Gerloff, 1967 accepted as Porterinema Waern, 1952
- Genus Sorapion Kuckuck, 1894
- Genus Zosterocarpus Bornet, 1890
- Class Phaeosacciophyceae
- Class Phaeothamniophyceae
- Class Picophagea accepted as Picophagophyceae
- Class Picophagophyceae
- Class Pinguiophyceae
- Class Raphidophyceae
- Class Schizocladiophyceae
- Class Synchromophyceae
- Class Synurophyceae accepted as Chrysophyceae
- Class Tribophyceae accepted as Xanthophyceae
- Class Xanthophyceae
- Family Ochrophyta incertae sedis
- Phylum Oomycota accepted as Pseudofungi
- Phylum Phaeophyta accepted as Ochrophyta
- Phylum Pseudofungi
- Phylum Raphidophyta accepted as Ochrophyta
- Phylum Sagenista accepted as Bigyra
- Phylum Xanthophyta accepted as Ochrophyta
- Subphylum Bigyromonada
- Class Bigyromonadea accepted as Developea
- Family Kaonashiidae Weston, Eglit & Simpson, 2023
- Infrakingdom Rhizaria
- Kingdom Fungi
- Kingdom Plantae
- Kingdom Protista accepted as Protozoa
- Kingdom Protozoa
- Kingdom Viruses
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