Science motivation and identity have been considered important in science education research literature. The role of science achievement between the motivation and identity has rarely been contemplated. Gender issues in science motivation, identity, and achievement have also been considered crucial. Although most studies hypothesized science identity would be a cause of motivation, there seems very few research that quantitatively examined their longitudinal relationship. Data from 186 students in a coeducational general high school in Seoul, Republic of Korea, was collected. Auto-regressive cross-lagged models were fitted without and with science achievement as a mediator. As results, it was shown that science motivation causes identity not the opposite. With science achievement, science motivation showed direct and indirect effects on science identity. By multiple-group analysis, it was shown that male students formulate their science identity indirectly from science motivation through the mediation of science achievement, and female students directly from science motivation.