Recently, medaka has been used as a model organism in various research fields. However, even though it possesses several advantages over zebrafish, fewer studies were done in medaka than zebrafish, especially its behaviour. Thus, to provide more information regarding its behaviour and to demonstrate the be-havioural differences between several species of medaka, we compared the behavioural performance and biomarker expression in the brain between four medaka fishes, which were Oryzias latipes, O. dancena, O. woworae, and O. sinensis. From the results, we found that each medaka species explicitly exhib-ited different behaviours to each other, which might be related to the different basal levels of several biomarkers. Furthermore, by phenomics and ge-nomic-based clustering, the differences between these medaka fishes were further investigated. Interestingly, even though both phenomics and ge-nomic-based clustering showed some resemblances to each other in terms of the interspecies relationship between medaka and zebrafish, however, in the medaka interspecies comparisons, this similarity was not displayed. Therefore, these results suggest a re-interpretation of several prior studies in comparative biology. We hope that these results contribute to the growing database of medaka fish phenotypes and provide one of the foundations for future phe-nomics studies of medaka fish.