Its subsequent taxonomic history has been complex, riddled with confusion with Trachylepis maculata and other species, homonyms, and other problems.

The species is classified in the otherwise mostly African genus Trachylepis and is thought to have reached its island from Africa by rafting.

[14] The species was first formally described by John Edward Gray in 1839,[3] based on two specimens collected by HMS Chanticleer before 1838.

Boulenger, in 1887 synonymized it under Mabuia punctata (the Noronha skink) without comment,[7] a position followed by H. Travassos with some doubt.

Burt resurrected the name Mabuya punctata (now spelled correctly) for the Noronha skink, noting that it was "apparently a very distinct species", but did not mention maculata,[9] and in 1935, E.R.

[22] He wrote that the Noronha skink was very distinct from other American Mabuya and more similar in some respects to African species.

[25] He also considered Mabouya punctatissima and Trachylepis (Xystrolepis) punctata Tschudi, 1845, described from Peru, as synonyms of this species.

"[20] In 2002, P. Mausfeld and D. Vrcibradic published a note on the nomenclature of the Noronha skink informed by a re-examination of Gray's original type specimens; despite extensive attempts to correctly name the species, they were apparently the first to do so since Boulenger in 1887.

[20] In the same year, Mausfeld and others conducted a molecular phylogenetic study on the Noronha skink, using the mitochondrial 12S and 16S rRNA genes, and showed that the species is more closely related to African than to South American Mabuya species,[29] as previously suggested on the basis of morphological similarities.

[31][fn 6] Additional molecular phylogenetic studies published in 2003 and 2006 confirmed the relationship between the Noronha skink and African Trachylepis.

[34] The Noronha skink is covered with light and dark spots above, but there is substantial variation in the precise colors.

[41] The Noronha skink has 26 presacral vertebrae (located before the sacrum), similar to most Trachylepis, but unlike American Mabuya, which have at least 28.

[50] Apart from T. atlantica, the reptile fauna of Fernando de Noronha consists of the indigenous amphisbaenian Amphisbaena ridleyi and two introduced lizards, the gecko Hemidactylus mabouia and the tegu Tupinambis merianae.

[52] The Noronha skink is oviparous (egg-laying), like many Trachylepis,[11] but unlike Mabuya, which are all viviparous (giving live birth).

[47] A geologist who visited the island in 1876[54] noted that the skink is curious and bold: While seated upon the bare rocks I have often observed these little animals watching me, apparently with as much curiosity as I watched them, turning their heads from side to side as if in an effort to be wise.

If I kept quiet for a few minutes they would creep up to me and finally upon me; if I moved, they ran down the faces of the rocks, and turning, stuck their heads above the edges to watch me.

[57] Analysis of stomach contents indicates that it mainly eats plant material, at least during the dry period,[58] but it also feeds on insects, including larvae, termites (Isoptera), ants (Formicidae), and beetles (Coleoptera).

[44] Its prey is mostly mobile, rather than sedentary,[59] which is consistent with the relatively high proportion of time it spends moving.

[57] Humans have introduced additional food sources to the island, including Acacia seeds, feces of the rock cavy (Kerodon rupestris), carrion flies, juvenile Hemidactylus mabouya, and even cookie crumbs given by tourists.

[63] In 1887, H. N. Ridley observed Noronha skinks eating banana skins and yolk from doves' eggs.

[64] Several cases of cannibalism have been reported, involving skinks eating eggs, juveniles, and the tail of an adult.

[68] Phylogenetic analyses using a variety of mitochondrial and nuclear genes places the Noronha skink among the tropical African species of Trachylepis,[69] a position also supported by morphological similarities.

[71] The South American and Caribbean Mabuya skinks form a clade that appears to be derived from a separate colonization from Africa.

Additionally, the urbanization of surrounding areas to the lizards habitat could be detrimental, therefore International Union for Conservation of Nature evaluated it as least concern.