In Drosophila, the RNA helicase VASA (VAS) is required for both germ line formation and oocyte differentiation. While the murine VAS homologue is required for spermatogenesis, it is dispensable for germ line formation. The molecular basis for this apparently dual role of VAS in germ line ontogeny is, however, unclear. Recent evidence indicates that fish, like flies, employs VAS both in early and late stages of the germ line development and that there is a sex-linked differential expression of splice variants. We show here that the longer of two splice variants of zebrafish vas is transiently downregulated in the germ line around the time when the germ cells reach the developing gonad. Using transgenic vas::EGFP fish lines, which allow us to distinguish between male and female individuals, we show that the long splice variant reappears in both sexes at around day 25 and is subsequently downregulated during male gonadal development. Our data further suggest that there is a switch from maternal to zygotic expression of the long splice variant of vas as sexual dimorphic development commences.