The preference intensities of Japanese Medaka (Japanese killifish, Oryzias latipes) to the three environmental factors of water depth, current velocity and cover were discussed in this paper. Mathematical models for preference intensities of Japanese Medaka to the three environmental factors were constructed by an on-the-spot examination executed ni an agricultural canal located at Sone-sinden, Kita-kyushu City, Fukuoka Prefecture, Japan. A simple genetic algorithm was introduced to search for the optimal functional representation of preference intensity. The results indicated that themaximum preference level of Japanese Medaka was determined at a water depth of 8 cm, a current velocity of 3.8 cm/s and a cover ratio of 38%. The relative weights of the environmental factors were evaluated as 0.092 for depth, 1.0 for velocity and 0.092 for cover, when the maximum weight was normalized to be unity. The weight values suggested that the environmental preferences of Japanese Medaka were almost equally affected by the three environmental factors. Judging from the good agreement between the predicted and observed distributions, the model could successfully predict the environmental preferences of Japanese Medaka.