The organization of the neuromuscular system of the dorsal and caudal fin of zebrafish, Danio rerio, was studied, including the anatomy of fin motoneurons as revealed by neurobiotin backfills and differential staining using fluorescent markers. The musculature of the dorsal fin consists of one pair of protractor and retractor muscles and 10 sets of muscles attaching to the bases of dorsal fin rays. Each set consists of one pair of erector, depressor, and inclinator muscles. The supplying nerves of the dorsal fin musculature originate from spinal segments 9-17 and form a dorsal fin plexus at the base of the muscles. Dorsal and caudal fin motoneurons have small cell bodies and ipsilateral dendritic branching patterns, thus resembling secondary motoneurons of the axial musculature. As shown by differential staining using fluorescent-labeled dextrans, cell bodies of dorsal fin motoneurons and axial motoneurons seem to be located in separate motor columns. The musculature of the caudal fin is composed of 12 muscles that are arranged in a superficial and a deep muscle layer. The nerves that supply the caudal fin musculature arise from the last five caudal segments of the spinal cord and form the caudal plexus. Neurobiotin backfills were performed on the dorsal caudal muscles, the medial caudal muscles, and the ventral caudal muscles. Most cell bodies of caudal fin motoneurons are small and are located in a ventral motor column. The organization of dorsal and caudal fin motoneurons is compared with the innervation of fins in other fish. J. Comp. Neurol. 497:702-716, 2006. © 2006 Wiley-Liss, Inc.