The natural habitat of A. thomasi is Sierra Leone, Liberia and Guinea, mainly in smaller streams.

The fish are typically found in slightly acidic, oxygen rich water with other west African cichlid genera such as Hemichromis and Pelvicachromis.

This species is found in forest streams, shaded by dense overhanging vegetation where the water is heavily stained with tannins from decaying organic matter and is coloured like tea.

[3] These pairs are territorial: the female selects a laying site on a leaf or flat rock which she and the male clean.

[2] The specific name of this species honours the English aquatic technician W. Thomas (born 1965, the collector of the type).