The corticotropin-releasing hormone (CRH) family consists of four paralogous genes, CRH and urocortins (UCNs) 1, 2, and 3. In a previous study, we analyzed CRH in the teleost model organism zebrafish and its transcript distribution in the embryonic brain. Here, we describe full-length cDNAs encoding urotensin 1 (UTS1), the teleost UCN1 ortholog, and UCN3 of zebrafish. Major expression sites of uts1 in adult zebrafish are the caudal neurosecretory system and brain. By using RT-PCR analysis, we show that uts1 mRNA is also present in ovary, maternally contributed to the embryo, and expressed throughout embryonic development. Expression of ucn3 mRNA was detected in a range of adult tissues and during developmental stages from 24 hours post fertilization onward. Analysis of spatial transcript distributions by whole-mount in situ hybridization revealed limited forebrain expression of uts1 and ucn3 during early development. Small numbers of uts1-synthesizing neurons were found in subpallium, hypothalamus, and posterior diencephalon, whereas ucn3-positive cells were restricted to telencephalon and retina. The brainstem was the main site of uts1 and ucn3 synthesis in the embryonic brain. uts1 Expression was confined to the midbrain tegmentum; distinct hindbrain cell groups, including locus coeruleus and Mauthner neurons; and the spinal cord. ucn3 Expression was localized to the optic tectum, serotonergic raphe, and distinct rhombomeric cell clusters. The prominent expression of uts1 and ucn3 in brainstem is consistent with proposed roles of CRH-related peptides in stress-induced modulation of locomotor activity through monoaminergic brainstem neuromodulatory systems.