As one of the three major chordate taxa, the highly diverse taxon, Tunicata has always played a key role in considerations of evolutionary origins of vertebrates, especially since several larger-scaled molecular phylogenetic analyses support the hypothesis that tunicates are the sister group to vertebrates. Molecular phylogenetic studies of the relationships within Tunicata are highly contradictory, and cladistic analyses of morphological characters for Tunicata remained limited. In order to come to a better understanding of chordate evolution, we comparatively investigated nine different tunicate species belonging to five different higher tunicate taxa: Phlebobranchiata, Aplousobranchiata, Stolidobranchiata, Thaliacea, and Appendicularia using immunofluorescence labeling with antibodies against serotonin in conjunction with confocal laser scanning microscopy. We found that adult ascidians are comparable in regard to their respective patterns of serotonin-like immunoreactive (serotonin-lir) cells, whereas the planktonic tunicates differ in several aspects. The distribution patterns of serotonin-lir cells in tunicates suggest that serotonin-like immunoreactivity can behave as an independent character during evolution. While the distribution pattern of serotonin-lir cells agrees well with classical taxonomic groupings, phylogenetic interpretation remains inconclusive, as ad hoc hypotheses are always necessary to explain contradictory character distribution. Based on light-microscopically observed morphology, we could distinguish three different types of serotonin-lir cells, most probably functionally distinctive. These were approximately spherical serotonin-lir cells, possibly involved in the control of ciliary beating and mucus secretion, elongated serotonin-lir cells potentially involved in hormonal regulation of feeding, and serotonin-lir neurons that might be implicated in the initiation of locomotory behavior.