Many classes of spinal interneurons in zebrafish have been described based on morphology, but their transmitter phenotypes are largely unknown. Here we combine back-filling or genetic labeling of spinal interneurons with in situ staining for markers of neurotransmitter phenotypes, including the vesicular glutamate transporter (VGLUT) genes for glutamatergic neurons, the neuronal glycine transporter (GLYT2) for glycinergic neurons, and glutamic acid decarboxylase (GAD) for GABAergic neurons. Neurons positive for VGLUT include the commissural CoPA, MCoD, UCoD, and some of the CoSA neurons. The CiD interneurons, which have ipsilateral descending axons, were also VGLUT-positive, as were the ventrally located VeMe interneurons, whose descending axonal trajectory has not been clearly revealed. Cells positive for GLYT2 include the commissural CoLAs as well as some of the CoBL and CoSA neurons. The CiA cells were the only GLYT2-positive cells with an ipsilateral axon. Cells staining for GAD included, most notably, the dorsal longitudinal ascending (DoLA) and KA interneurons. Our approach allowed us to define the likely transmitter phenotypes of most of the known classes of spinal interneurons. These data provide a foundation for understanding the functional organization of the spinal networks in zebrafish. J. Comp. Neurol. 480:19–37, 2004. © 2004 Wiley-Liss, Inc.