Studies of ion regulation by mitochondria-rich cells (MRCs) of transport epithelia in fish have revealed many processes by which ion homeostasis is achieved. However, the control of these mechanisms and, particularly, the extent of nervous system involvement are not completely understood. We characterized the potential innervation of MRCs in various gill and extrabranchial tissues involved in ion transport in the model vertebrate the zebrafish. Confocal and conventional microscopy of whole-mount preparations were combined with immunofluorescence techniques to label MRCs with antibodies against a subunit of the enzyme Na+/K+-ATPase and nerve fibers with a zebrafish neuronal marker, zn-12. MRCs of the gill filaments were identified by their morphology and migration out to the lamellae in response to ion-poor water acclimation. Gill MRCs were intimately associated with nerve fibers originating from outside the filaments. MRCs of the opercular epithelium resembled those of the gill and were also located adjacent to nerve fibers. Mitochondria-rich “pseudobranch cells” were identified in the pseudobranch by immunofluorescence and labeling of dissociated cells with the mitochondrial marker DASPEI. Pseudobranch MRCs resembled gill MRCs and received innervation from a dense network of nerve fibers. In larvae, MRCs were distributed across the surface of the skin. These cells were situated among a dense network of varicose nerve fibers, and some MRCs of the skin displayed extensive cytoplasmic processes. Evidence is presented suggestive of widespread association of MRCs with the nervous system in transport epithelia and the neural control of MRC-mediated ion regulation in teleost fish. J. Comp. Neurol. 497:817-832, 2006. © 2006 Wiley-Liss, Inc.