The distribution, morphology and nuclear subdivisions of the cholinergic, putative catecholaminergic and serotonergic systems within the brains of two species of African mole-rat (Cape dune mole-rat -Bathyergus suillus; highveld mole-rat -Cryptomys hottentotuspretoriae) were identified following immunohistochemistry for acetylcholinesterase, tyrosine hydroxylase and serotonin. The aim of the present study was to investigate possible differences in the complement of nuclear subdivisions of these systems by comparing those of the mole-rats to published studies of other rodents. The mole-rats used exhibit a major reduction of the visual system and live a subterranean lifestyle. These wild caught animals also have differing social systems, the Cape dune mole-rat is strictly solitary whereas the highveld mole-rat occurs in social familial units. While these differences, especially that of phenotype, may lead to the prediction of significant differences in the nuclear complement of these systems, we found that all nuclei identified in all three systems in the laboratory rat and other rodents had direct homologs in the brains of the mole-rats studied. There were no additional nuclei in the brains of the mole-rats that are not found in the laboratory rat or other rodents and vice versa. The mole-rats are phylogenetically distant from the laboratory rat, but are still part of the order Rodentia. We conclude that changes in the nuclear organization of the systems studied appear to demonstrate a form of constraint related to the phylogenetic level of the order.