ABSTRACT The current study documents the findings from immunohistochemical examination of the brains of microbats and megabats (Chiroptera) using antibodies for cholineacetyltransferase (cholinergic neurons), tyrosine hydroxylase (dopaminergic, adrenergic and noradrenergic neurons), and serotonin (serotonergic neurons). The objective of the study was firstly to describe the anatomical organization and morphology of the neuromodulatory systems (nuclear complement) in both microbats and megabats, as there is no literature on these systems in the brains of chiropterans. Secondly, we aimed to investigate whether or not there are differences in these systems between the two suborders of chiroptera in hopes to shed some light on the phylogeny of the two, which is a controversial subject. The two groups were found to possess clear differences in their respective neuromodulatory nuclear complements. The differences observed between the two groups include a dorsal division of the locus coeruleus (A6d), which was absent in microbats but present in megabats, also the absence of an A4 in microbats but clear presence in megabats, and the parabigeminal (PBg) nucleus that was absent in microbats but clearly visible in megabats. The microbats were found to possess a complement that appeared similar to that of insectivores; whereas megabats had a complement resembling that of primates, carnivores and rodents. The differences found between the two groups suggest a diphyletic origin for the two groups.