Genetic relationships and variation in meristic counts, body shape and colour were examined in a large sample of Symphysodon collected from several locations in floodplain habitats along the length of the Amazon River. Surprisingly, mitochondrial DNA indicates no difference between the two historically described species, Symphysodon discus and Symphysodon aequifasciatus, but shows that non-clinal variation exists with a distinct lineage found in the western Amazon. This lineage is consistent with a colour form that is distinct from other Symphysodon lineages. This form has a parapatric distribution and is recognized as a distinct species, Symphysodon tarzoo. Adaptation to floodwater habitats supports genetic cohesion across a large range preventing fine scale regional diversification of the genus. Possible explanations for the unusual set of distributions for genetic and colour characters relate to the history of the Amazon basin and the probable division of lowland species when submerged geologic arches influence surface topology.