The purpose of both the (primary) bioluminescence (from aequorins action on luciferin) and the (secondary) fluorescence of GFP in jellyfish is unknown. GFP is co-expressed with aequorin in small granules around the rim of the jellyfish bell. The secondary excitation peak (480 nm) of GFP does absorb some of the blue emission of aequorin, giving the bioluminescence a more green hue. The serine 65 residue of the GFP chromophore is responsible for the dual-peaked excitation spectra of wild-type GFP. It is conserved in all three GFP isoforms originally cloned by Prasher. Nearly all mutations of this residue consolidate the excitation spectra to a single peak at either 395 nm or 480 nm. The precise mechanism of this sensitivity is complex, but, it seems, involves donation of a hydrogen from serine 65 to glutamate 222, which influences chromophore ionization. Since a single mutation can dramatically enhance the 480 nm excitation peak, making GFP a much more efficient partner of aequorin, A. victoria appears to evolutionarily prefer the less-efficient, dual-peaked excitation spectrum. Roger Tsien has speculated that varying hydrostatic pressure with depth may affect serine 65s ability to donate a hydrogen to the chromophore and shift the ratio of the two excitation peaks.  Thus, the jellyfish may change the color of its bioluminescence with depth. However, a collapse in the population of jellyfish in Friday Harbor, where GFP was originally discovered, has hampered further study of the role of GFP in the jellyfish's natural environment.
Most species of lancelet are known to produce GFP in various regions of their body. Unlike A. victoria, lancelets do not produce their own blue light, and the origin of their endogenous GFP is still unknown. Some speculate that it attracts plankton towards the mouth of the lancelet, serving as a passive hunting mechanism. It may also serve as a photoprotective agent in the larvae, preventing damage caused by high-intensity blue light by converting it into lower-intensity green light. However, these theories have not been tested.
GFP-like proteins have been found in multiple species of marine copepods, particularly from the Pontellidae and Aetideidae families. GFP isolated from Pontella mimocerami has shown high levels of brightness with a quantum yield of 0.92, making them nearly two-fold brighter than the commonly used EGFP isolated from A. victoria.