We report the isolation of two novel zebrafish mix-type homeobox genes, mtx1 and mtx2. The homeodomains of both Mtx1 and Mtx2 exhibited a 50% amino acid identity to other Mix-family protein homeodomains, mtx1 was expressed throughout the yolk syncytial layer (YSL), an extraembryonic structure in teleosts, from the late-blastula to the mid-gastrula period. mtx2 was first expressed in the dorsal blastomeres soon after the mid-blastula transition, and slightly later in the entire blastoderm margin. After the late blastula period, mtx2 transcripts were detected in the YSL, and they were restricted to the dorsal YSL by the early gastrula period. The expression of mtx2 was dependent on Wnt signals but not on Nodal signals, mtx1 expression was not regulated by either Wnt or Nodal signals. This is in complete contrast to the Nodal signal-dependent expression of mixer. These results indicate the complexity of the regulation of mix-type homeobox genes.