The spatial and temporal expression patterns of Strongylocentrotus purpuratus genes encoding four different transcription factors, viz. SpFoxb, SpHes, SpKrl, and SpNk1, have been examined, using a recently developed, highly sensitive whole mount in situ hybridization procedure, and quantitative real time PCR. Two of the genes studied, SpHes and SpNk1, are newly isolated. Their expression patterns suggest the existence of previously unknown ectodermal domains. Re-examination of the expression pattern of SpFoxb reveals domains of expression not previously reported for this gene, and we also provide a more detailed, temporal and spatial description of the expression pattern of SpKrl than heretofore available.