Brain-derived neurotrophic factor (BDNF) is a neurotrophin involved in the development and maintenance of vertebrate nervous systems. Although there were several studies in classical animal models, scarce information for fish was available. The main purpose of this study was to analyze the distribution of BDNF in the brain and retina of the cichlid fish Cichlasoma dimerus. By immunohistochemistry we detected BDNF-like immunoreactive cells in the cytoplasm and the nuclei of the ganglion cell layer and the inner nuclear layer of the retina. In the optic tectum, BDNF-like immunoreactivity was detected in the nucleus of neurons of the stratum periventriculare and the stratum marginale and in neurons of the intermediate layers. In the hypothalamus we found BDNF-like immunoreactivity mainly in the cytoplasm of the nucleus lateralis tuberis and the nucleus of the lateral recess. To confirm the nuclear and cytoplasm localization of BDNF we performed subcellular fractionation, followed by Western blot, detecting a 39 kDa immunoreactive-band corresponding to a possible precursor form of BDNF in both fractions. BDNF-like immunoreactivity was distributed in areas related with photoreception (retina), the integration center of retinal projections (optic tectum) and the control center of background and stress adaptation (hypothalamus). These results provide baseline anatomical information for future research about the role of neurotrophins in the adult fish central nervous system.