The males have a brilliant blue cap; some have black, others have green body plumage, but the relationship between the subspecies is not well understood.

The blue-capped manakin was formally described in 1825 by the German naturalist Johann Baptist von Spix under the binomial name Pipra coronata.

The type locality is the state of São Paulo de Olivença in western Brazil.

[4] The blue-capped manakin is now the type species of the genus Lepidothrix that was introduced by the French naturalist Charles Lucien Bonaparte in 1854.

Bond & Meyer de Schauensee, 1940) With the exception of L. c. carbonata, the subspecies categories listed above are not supported phylogenetically.

Blue-capped manakins differ genetically into six clades based on geographic location: trans-Andean, Venezuela, North Amazon, Napo-Marañon, Central Peru, and South Peru/Bolivia.

[8] Based on significant vocal and phylogenetic differences, in July 2022 the South American Classification Committee of the American Ornithological Society split L. c. velutina and L. c. minuscula from L. coronata and named the resulting L. velutina the velvety manakin.

They also renamed the now-reduced L. carbonata "blue-capped manakin" to avoid confusion with the pre-split species.

Physical boundaries, such as large Amazonian rivers and the Andes Mountains, tend to separate genetically distinct blue-capped manakins.

The uplift of the Andes Mountains seem to be the first major source of separation between blue-capped manakin populations followed by the establishment of Amazonian rivers.

Large rivers present a barrier to Blue-crowned manakins despite being flighted because they prefer the understory of terra firme (non-flooded) forests.

[8] Blue-capped manakins show sexual dimorphism in weight and wing chord length.

[16] Blue-capped manakins live in terra firme forest understory of South America.

[17] They chose small shrubs and treelets that are less than 1 meter tall and place their nests on horizontal forks.

[17][18] They typically nest in Rudgea spp., Ixora killipii, R. viridifoliax, and R. lindenicana along small ravines.

They forage in the understory between a height of 2–7 m. Their preferred food while in flocks are arthropods, including ants, flies, and other small insects.

Considering their normally frugivorous diet, it is speculated that the blue-capped manakins are taking advantage of the flock's ability to cause insects to scatter.

It is uncertain how blue-crowned manakins maintain population size with such a low rate of success, but it has been speculated that high female survivability and multiple breeding attempts per season may be a factor.

A genetic study revealed that half of the sampled manakins were infected with blood parasites, representing nine different types.