The auto-fluorescence patterns of the medusae observed under a fluorescent microscope with blue light excitation allows to distinguish two species of Eugymnanthea, this even when they are still attached to the hydroid as small medusa buds despite the occurrence of a sex-dependant pattern in E. japonica. A total of four distribution patterns of green fluorescence, including non-fluorescence, could be found. Three of them are found in E. japonica, called ‘subumbrellar fluorescence type’ except for non-fluorescence, while another type is found in E. inquilina, called ‘umbrellar margin fluorescence type’. During the short life of the medusa the latter type remained invariable for up to six days in E. inquilina, while the pattern observed for up to seven days in E. japonica changed sometimes, but it always remained distinguishable from the pattern found in E. inquilina. Therefore, the fluorescence pattern is a reliable taxonomic character. Fluorescence was not found in unfertilized eggs, planulae 2–8 days old, parthenogenetically produced larvae, or in the hydroids of the two species. The auto-fluorescent and possible bioluminescent tissues of these Eugymnanthea medusae could have some unknown biological significance.