We have characterised the expression of four genes coding for Forkhead box-containing ('Fox') transcription factors identified from the hydrozoan (Leptomedusa) Clytia hemisphaerica. Phylogenetic analyses including all available non-bilaterian Fox sequences placed these genes in subfamilies B, Q2 (two genes) and O, and indicated that at least 17 Fox subfamilies were present in the common cnidarian/bilaterian ancestor, with multiple subsequent losses in cnidarian lineages. Chordate FoxB and FoxQ2A subfamily genes show polarised expression in early embryos. Correspondingly, Clytia CheFoxB expression was localised around the gastrulation site (future oral pole) at blastula and gastrula stages, with CheFoxQ2a expressed in a complementary aboral domain, maintained through larval development. Distinct later expression domains were observed for CheFoxB in the larval endoderm region, and in the statocyst, gonad and tentacle bulb of the medusa. A second Clytia FoxQ2 gene, CheFoxQ2b, not expressed in the embryo, larva or polyp, was detected uniquely in the gonads of the medusa. In contrast, CheFoxO, whose sequence indicates regulation by the PI3-Kinase/PKB signalling pathway consistent with known roles in bilaterian developmental regulation, was detected throughout the Clytia life cycle. CheFoxO expression was enhanced in regions associated with growth control including larval poles, gonad and the margin of the medusa bell. These results support the idea that an early embryonic patterning system involving FoxB and FoxQ2 family genes has been evolutionary conserved and indicate that Fox family genes have also acquired distinct roles during other phases of the hydrozoan life cycle.