The Cephalochordata is traditionally seen as a sister subphylum to the vertebrates, with which it is grouped together into a clade (sometimes called Notochordata) which in turn is the sister group to the simpler still Urochordata.
Newer research suggests this is not the case.
The Cephalochordata is the most basal subphylum of the chordates, while the sister group of the vertebrates are the tunicates, previously known as the urochordates.
However, older molecular studies placed cephalochordates nearer to vertebrates, and "[m]ost authors regard amphioxus as the closest relative of the Vertebrata on the basis of 10–15 [morphological] features that are not seen in tunicates".

Among the three extant (living) genera, Asymmetron is basal and it is placed in its own family.
Genetic studies have come to separate conclusions on their divergence, with some suggesting that Asymmetron diverged from other lancelets more than 100 million years ago and others (with higher statistic support) that it occurred about 42 million years ago.
The two remaining genera, Branchiostoma and Epigonichthys diverged from each other about 36 million years ago.
Despite this deep separation, hybrids between Asymmetron lucayanum and Branchiostoma floridae are viable (among the deepest split species known to be able to produce such hybrids).

The following are the species recognised by ITIS.
Other sources recognize about thirty species.
It is likely that currently unrecognized cryptic species remain.

Order Branchiostomiformes
Family Asymmetronidae 
Genus Asymmetron Andrews 1893 [Amphioxides Gill 1895]
Asymmetron inferum Nishikawa 2004
Asymmetron lucayanum Andrews 1893 (Sharptail lancelet)
Family Epigonichthyidae Peters 1876
Genus Epigonichthys Peters 1876 [Amphipleurichthys Whitley 1932; Bathyamphioxus Whitley 1932; Heteropleuron Kirkaldy 1895; Merscalpellus Whitley 1932; Notasymmetron Whitley 1932; Paramphioxus Haekel 1893; Zeamphioxus Whitley 1932]
Epigonichthys australis (Raff 1912)
Epigonichthys bassanus (Günther 1884)
Epigonichthys cingalensis (Kirkaldy 1894); nomen dubium
Epigonichthys cultellus Peters 1877
Epigonichthys hectori (Benham 1901) (Hector's lancelet)
Epigonichthys maldivensis (Foster Cooper 1903)
Family Branchiostomidae Bonaparte 1841
Genus Branchiostoma Costa 1834 non Newport 1845 non Banks 1905 [Amphioxus Yarrell 1836; Limax Pallas 1774 non Linnaeus 1758 non Férussac 1819 non Martyn 1784; Dolichorhynchus Willey 1901 non Mulk & Jairajpuri 1974]
Branchiostoma africae Hubbs 1927
Branchiostoma arabiae Webb 1957
Branchiostoma bazarutense Gilchrist 1923
Branchiostoma belcheri Gray 1847 (Belcher's lancelet)
Branchiostoma bennetti Boschung & Gunter 1966 (Mud lancelet)
Branchiostoma bermudae Hubbs 1922
Branchiostoma californiense Andrews 1893 (Californian lancelet)
Branchiostoma capense Gilchrist 1902
Branchiostoma caribaea Sundevall 1853 (Caribbean lancelet)
Branchiostoma clonasea 
Branchiostoma elongata Sundevall 1852
Branchiostoma floridae Hubbs 1922 (Florida lancelet)
Branchiostoma gambiense Webb 1958
Branchiostoma indica Willey 1901
Branchiostoma japonica Willey 1896  (Pacific lancelet)
Branchiostoma lanceolata Pallas 1774 (European lancelet)
Branchiostoma leonense Webb 1956
Branchiostoma longirostra Boschung 1983 (Shellhash lancelet)
Branchiostoma malayana Webb 1956
Branchiostoma moretonense Kelly 1966; nomen dubium
Branchiostoma nigeriense Webb 1955
Branchiostoma platae Hubbs 1922
Branchiostoma senegalense Webb 1955
Branchiostoma tattersalli Hubbs 1922
Branchiostoma virginiae Hubbs 1922 (Virginian lancelet)
The Cephalochordata is traditionally seen as a sister subphylum to the vertebrates, with which it is grouped together into a clade (sometimes called Notochordata) which in turn is the sister group to the simpler still Urochordata. Newer research suggests this is not the case. The Cephalochordata is the most basal subphylum of the chordates, while the sister group of the vertebrates are the tunicates, previously known as the urochordates. However, older molecular studies placed cephalochordates nearer to vertebrates, and "[m]ost authors regard amphioxus as the closest relative of the Vertebrata on the basis of 10–15 [morphological] features that are not seen in tunicates".
Among the three extant (living) genera, Asymmetron is basal and it is placed in its own family. Genetic studies have come to separate conclusions on their divergence, with some suggesting that Asymmetron diverged from other lancelets more than 100 million years ago and others (with higher statistic support) that it occurred about 42 million years ago. The two remaining genera, Branchiostoma and Epigonichthys diverged from each other about 36 million years ago. Despite this deep separation, hybrids between Asymmetron lucayanum and Branchiostoma floridae are viable (among the deepest split species known to be able to produce such hybrids).
The following are the species recognised by ITIS. Other sources recognize about thirty species. It is likely that currently unrecognized cryptic species remain.
Order Branchiostomiformes
Family Asymmetronidae 
Genus Asymmetron Andrews 1893 [Amphioxides Gill 1895]
Asymmetron inferum Nishikawa 2004
Asymmetron lucayanum Andrews 1893 (Sharptail lancelet)
Family Epigonichthyidae Peters 1876
Genus Epigonichthys Peters 1876 [Amphipleurichthys Whitley 1932; Bathyamphioxus Whitley 1932; Heteropleuron Kirkaldy 1895; Merscalpellus Whitley 1932; Notasymmetron Whitley 1932; Paramphioxus Haekel 1893; Zeamphioxus Whitley 1932]
Epigonichthys australis (Raff 1912)
Epigonichthys bassanus (Günther 1884)
Epigonichthys cingalensis (Kirkaldy 1894); nomen dubium
Epigonichthys cultellus Peters 1877
Epigonichthys hectori (Benham 1901) (Hector's lancelet)
Epigonichthys maldivensis (Foster Cooper 1903)
Family Branchiostomidae Bonaparte 1841
Genus Branchiostoma Costa 1834 non Newport 1845 non Banks 1905 [Amphioxus Yarrell 1836; Limax Pallas 1774 non Linnaeus 1758 non Férussac 1819 non Martyn 1784; Dolichorhynchus Willey 1901 non Mulk & Jairajpuri 1974]
Branchiostoma africae Hubbs 1927
Branchiostoma arabiae Webb 1957
Branchiostoma bazarutense Gilchrist 1923
Branchiostoma belcheri Gray 1847 (Belcher's lancelet)
Branchiostoma bennetti Boschung & Gunter 1966 (Mud lancelet)
Branchiostoma bermudae Hubbs 1922
Branchiostoma californiense Andrews 1893 (Californian lancelet)
Branchiostoma capense Gilchrist 1902
Branchiostoma caribaea Sundevall 1853 (Caribbean lancelet)
Branchiostoma clonasea 
Branchiostoma elongata Sundevall 1852
Branchiostoma floridae Hubbs 1922 (Florida lancelet)
Branchiostoma gambiense Webb 1958
Branchiostoma indica Willey 1901
Branchiostoma japonica Willey 1896  (Pacific lancelet)
Branchiostoma lanceolata Pallas 1774 (European lancelet)
Branchiostoma leonense Webb 1956
Branchiostoma longirostra Boschung 1983 (Shellhash lancelet)
Branchiostoma malayana Webb 1956
Branchiostoma moretonense Kelly 1966; nomen dubium
Branchiostoma nigeriense Webb 1955
Branchiostoma platae Hubbs 1922
Branchiostoma senegalense Webb 1955
Branchiostoma tattersalli Hubbs 1922
Branchiostoma virginiae Hubbs 1922 (Virginian lancelet)
Lancelet