In a search for zebrafish genes expressed during early stages of development, we have identified two ESTs encoding proteins related to Drosophila mago nashi. Zebrafish mago nashi codes for a small protein with no clearly identified functional domains, and which is highly conserved during evolution. This paper describes the identification and a detailed gene expression analysis of zebrafish mago nashi during development. Our results demonstrate that mago nashi encodes a maternal transcript detected in both blastomeres and yolk cell at the 1-2 cell stages, and in the blastoderm during segmentation. We show that a putative microtubule-mediated transport of mago nashi mRNA from the vegetal hemisphere into animal blastomeres determines the localization of the transcript in the animal pole, immediately after fertilization. Furthermore, the microtubule array contained into the yolk cell seems to be responsible for the high level of mago nashi transcript detected in the central blastomeres at the 8-16 cell stages. Zygotic mago nashi is expressed into the dorsal-marginal region during gastrulation, and starting from somitogenesis to 24 hpf, the expression domain becomes progressively restricted to the developing neural tube and paraxial structures, and ventrally to the pronephric ducts.