The forkhead proteins (Fox) act as transcription factors in many biological processes in a wide range of species. One member of this superfamily, Foxg1, has essential roles in the development of eyes, telencephalon, ears and olfactory system. Zebrafish foxg1 has been reported to have similar roles as the mouse orthologue Foxg1. However, no data has been reported about possible zebrafish foxg1 paralogues. In this study we identified one zebrafish foxg1 paralogue by enhancer trapping, which we designate foxg1b. A more diverged paralogue, foxg1c, was identified by homology searches. Sequence comparisons indicate that both foxg1b and foxg1c are less related to mouse than the previously characterized foxg1. We report that foxg1b is expressed in a regionally restricted pattern within the developing eye, mainly in the dorsal-nasal retina, which is similar to the retinal expression of mouse Foxg1. By contrast, foxg1c is only expressed transiently in the eyes and forebrain between 14 and 20h post-fertilization, while expression was detected exclusively in the developing inner ear at later stages. Our results suggest that foxg1b and foxg1c have undergone expression pattern divergence during evolution that has resulted in functional specialization.