Organisms in the order of Siphonophorae have been classified into the phylum Cnidaria and the class Hydrozoa.
The phylogenetic relationships of siphonophores have been of great interest due to the high variability of the organization of their polyp colonies and medusae.
Once believed to be a highly distinct group, larval similarities and morphological features have led researchers to believe that siphonophores had evolved from simpler colonial hydrozoans similar to those in the orders Anthoathecata and Leptothecata.
Consequently, they are now united with these in the subclass Hydroidolina.

Early analysis divided siphonophores into 3 main subgroups based on the presence or the absence of 2 different traits: swimming bells (nectophores) and floats (pneumatophores).
The subgroups consisted of Cystonectae, Physonectae, and Calycorphores.
Cystonectae had pneumatophores, physonectae had nectophores, and calycophores had both.

Eukaryotic nuclear small subunit ribosomal gene 18S, eukaryotic mitochondrial large subunit ribosomal gene 16S, and transcriptome analyses further support the phylogenetic division of Siphonophorae into 2 main clades: Cystonectae and Codonophora.
Suborders within Codonophora include Physonectae (consisting of the clades Calycophorae and Euphysonectae), Pyrostephidae, and Apolemiidae.

Suborder Calycophorae
Abylidae Agassiz, 1862
Clausophyidae Totton, 1965
Diphyidae Quoy & Gaimard, 1827
Hippopodiidae Kölliker, 1853
Prayidae Kölliker, 1853
Sphaeronectidae Huxley, 1859
Tottonophyidae Pugh, Dunn & Haddock, 2018
Suborder Cystonectae
Physaliidae Brandt, 1835
Rhizophysidae Brandt, 1835
Suborder Physonectae
Agalmatidae Brandt, 1834
Apolemiidae Huxley, 1859
Cordagalmatidae Pugh, 2016
Erennidae Pugh, 2001
Forskaliidae Haeckel, 1888
Physophoridae Eschscholtz, 1829
Pyrostephidae Moser, 1925
Resomiidae Pugh, 2006
Rhodaliidae Haeckel, 1888
Stephanomiidae Huxley, 1859
Organisms in the order of Siphonophorae have been classified into the phylum Cnidaria and the class Hydrozoa. The phylogenetic relationships of siphonophores have been of great interest due to the high variability of the organization of their polyp colonies and medusae. Once believed to be a highly distinct group, larval similarities and morphological features have led researchers to believe that siphonophores had evolved from simpler colonial hydrozoans similar to those in the orders Anthoathecata and Leptothecata. Consequently, they are now united with these in the subclass Hydroidolina.
Early analysis divided siphonophores into 3 main subgroups based on the presence or the absence of 2 different traits: swimming bells (nectophores) and floats (pneumatophores). The subgroups consisted of Cystonectae, Physonectae, and Calycorphores. Cystonectae had pneumatophores, physonectae had nectophores, and calycophores had both.
Eukaryotic nuclear small subunit ribosomal gene 18S, eukaryotic mitochondrial large subunit ribosomal gene 16S, and transcriptome analyses further support the phylogenetic division of Siphonophorae into 2 main clades: Cystonectae and Codonophora. Suborders within Codonophora include Physonectae (consisting of the clades Calycophorae and Euphysonectae), Pyrostephidae, and Apolemiidae.
Suborder Calycophorae
Abylidae Agassiz, 1862
Clausophyidae Totton, 1965
Diphyidae Quoy & Gaimard, 1827
Hippopodiidae Kölliker, 1853
Prayidae Kölliker, 1853
Sphaeronectidae Huxley, 1859
Tottonophyidae Pugh, Dunn & Haddock, 2018
Suborder Cystonectae
Physaliidae Brandt, 1835
Rhizophysidae Brandt, 1835
Suborder Physonectae
Agalmatidae Brandt, 1834
Apolemiidae Huxley, 1859
Cordagalmatidae Pugh, 2016
Erennidae Pugh, 2001
Forskaliidae Haeckel, 1888
Physophoridae Eschscholtz, 1829
Pyrostephidae Moser, 1925
Resomiidae Pugh, 2006
Rhodaliidae Haeckel, 1888
Stephanomiidae Huxley, 1859
Siphonophorae