The general organization of the cholinergic system in the central nervous system is similar among vertebrates, though fish show higher variability. Thus, in zebrafish, cholinergic cells are absent from the habenula and the rhombencephalic reticular formation, where such neurons are present in most vertebrate species analyzed. In this work, we compared the distribution of choline acetyltransferase in the central nervous system of both zebrafish and tench, in order to investigate whether these divergences in the distribution of cholinergic cells in zebrafish are species-specific, or a feature shared by members of the cyprinid family. Our data show that these two cyprinid possess in common some peculiarities in their cholinergic system that are not present in the rest of fish analyzed (e.g. absence of cholinergic cells in the habenula and their presence in the descendent octaval nucleus). Nonetheless, some cholinergic cells were observed in the dorsal thalamus and rhombencephalic reticular nuclei of the tench, which were absent in the same regions in zebrafish. The comparative analysis suggests a divergent evolution of the cholinergic system among close-related cyprinid species.