The purposes of this study were to investigate students' conceptual learning outcomes and the effect of motivation on students' conceptual learning outcomes in two different contexts: a Web-based and a classroom-based instruction, which incorporated the Dual Situation Learning Model (DSLM). Nine classes of Grade eight students (N = 190) were involved in the study; five classes participated in a Web-based context and four classes in a regular classroom-based context. The topic covered was chemical reaction. Students' conceptual change outcomes were assessed using eight two-tier pre/post conceptual tests during the instruction and the reaction rate integrated conceptual test at the end of the instruction. Students' motivation data were collected in the beginning and during instruction using the items from the Students' Motivation Toward Science Learning (SMTSL) questionnaire. The data were analyzed using ANOVA, ANCOVA, bivariate correlation, and multiple regression analysis. Findings revealed that students' motivational factors were correlated significantly with their conceptual learning outcomes in both Web-based and classroom-based science teaching. In the Web-based context, students' motivation during the Web-based learning played a more important role on students' conceptual learning outcomes than before learning.