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This longitudinal study validated a two-dimensional measure of stereotype threat with two samples of underrepresented science undergraduates. Confirmatory factor analyses supported the multidimensionality of stereotype threat and suggested students distinguished between self-reputation and group-reputation stereotype threats. Results of multi-group and longitudinal measurement invariance tests suggested that the two-dimensional measure was structurally stable across groups and time. Chemistry, compared to biology, students indicated higher levels of both stereotype threats. Students in both courses started the semester with higher perceptions of group-reputation than self-reputation threat. The two beliefs developed similarly in the two classes. Overall, our study supports the existence of distinct stereotype threats and provides evidence for a valid measure for assessing this multi-dimensional phenomenon in various science fields.