LIM-homeodomain (LIM-hd) proteins form a multifunctional family of transcription factors that plays critical roles in the development of progenitor and post-mitotic cells. Considerable work has focused on what regulates their expression post-mitotically in the spinal cord. However, little is known about what regulates LIM-hd genes at earlier developmental stages. To address this question, we explored the role of fibroblast growth factor (FGF) signalling in regulating the expression of a Xenopus laevis Lhx9 orthologue (XLhx9). XLhx9 is first expressed in the eye field and hindbrain, and when FGF receptor (FGFR) activation was inhibited prior to its onset, both brain and eye field expression was diminished. However, when FGFRs were inhibited after XLhx9 onset, retinal expression remained strong and brain expression was again diminished. These data suggest that while FGF signalling initiates and maintains brain XLhx9 expression, in the eye primordium the requirement of FGFs for expression is rapidly lost.