The forkhead transcription factor gene family encodes a large group of proteins that play critical roles in many developmental events. In this report, we describe the isolation and characterization of foxp1 in zebrafish. The full-length zebrafish foxp1 cDNA contains 2,440 bp encoding a protein of 659 amino acids which shares 72, 68, 68, 70, 65, and 62% overall identity with human, mouse, rat, chicken, zebra finch, and frog Foxp1, respectively. Results of whole-mount in situ hybridization showed that foxp1 exhibits very complex and dynamic expression pattern during early embryonic development. Prominent foxp1 expression is detected in many regions of the developing central nervous system, especially in midbrain-hindbrain boundary, hindbrain, and spinal cord. Strong expression is also observed in retina, ear, branchial arches, hatching gland, heart, pronephric duct, gut, proctodeum, pectoral fin, and swim bladder. These results provide evidence that foxp1 is likely to function as a very important transcription factor in the development of the central nervous system and many other organs in zebrafish.