Abstract Background Green fluorescent protein (GFP) has been found in a wide range of Cnidaria, a basal group of metazoans in which it is associated with pigmentation, fluorescence, and light absorbance. A GFP has been recently discovered in the pigmentless chordate Branchiostoma floridae (amphioxus) that shows intense fluorescence mainly in the head region. Results The amphioxus genome encodes 16 closely-related GFP-like proteins, all of which appear to be under purifying selection. We divide them into 6 clades based on protein sequence identity and show that representatives of each clade have significant differences in fluorescence intensity, extinction coefficients, and absorption profiles. Furthermore, GFPs from two clades exhibit antioxidant capacity. We therefore propose that amphioxus GFPs have diversified their functions into fluorescence, redox, and perhaps just light absorption in relation to pigmentation and/or photoprotection. Conclusion The rapid radiation of amphioxus GFP into clades with distinct functions and spectral properties reveals functional plasticity of the GFP core. The high sequence similarities between different clades provide a model system to map sequence variation to functional changes, to better understand and engineer GFP.