Vertebrate homeobox genes have been identified on the basis of sequence homology to Drosophila segmentation and homeotic genes. We have analyzed the spatial distribution patterns in hatching larvae of transcripts from two different types of zebrafish (Brachydanio rerio) homeobox genes. Tritiated DNA fragments from one zebrafish gene (ZF-21) of the Antennapedia-class and one (ZF-EN) of the engrailed-type were used as probes to detect transcripts in larval tissue sections. Both zebrafish genes are expressed mainly in spatially restricted regions of the central nervous system. The transcripts from ZF-21 was detected in the posterior part of the hindbrain, and ZF-EN was found to be most intensively expressed in a restricted domain located in the region of the junction between the mid- and hindbrain. These neural expression patterns are very similar to those of the homologous murine genes Hox-2.1 and En-2 and clearly suggest a strong functional conservation.