There are at least three recognized subspecies (Stiles 1999):
H. j. jacula Gould 1850 (eastern Panama to northern and central Colombia): See Detailed Description.
H. j. henryi Lawrence 1867 (Costa Rica and western Panama): This subspecies is larger than the nominate, and males have more brilliant glittering plumage areas; the green plumage is paler with little or no bluish tinge; tail of male entirely blue-black; females are more extensively white below with bright green spotting laterally.
H. j. jamesoni (Bourcier 1851) (southwestern Colombia to western Ecuador): Males of this subspecies are much duller green on the crown, throat, and breast; the central rectrices are glossed with green, and its tail is shorter than that of the nominate.
In hummingbird phylogenetics, the genus Heliodoxa forms part of the Andean clade (Bleiweiss et al. 1997, McGuire et al. 2007), with the Green-crowned Brilliant being the only Heliodoxa species to have spread to Central America (Gerwin and Zink 1989, McGuire et al. 2007). Phylogenetic studies indicate that the Green-crowned Brilliant is closely related to the Violet-fronted Brilliant (H. leadbeateri), which together form a sister group to the Fawn-breasted Brilliant (H. rubinoides) (Gerwin and Zink 1989, McGuire et al. 2007).
A presumed hybrid of the Green-crowned Brilliant (probably subspecies jamesoni) and Fawn-breasted Brilliant has been noted in Cauca department in southwestern Colombia (Donegan and Dávalos 1999).