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This study integrated understandings from Achievement Goal Theory and Social Identity Theory in order to investigate the relations between perceived teachers’ emphasis on mastery and performance goals – achievement goal structures – and students’ bias towards cooperating with peers who are similar to them. The study followed 100 students as they made the transition from elementary to Junior High School. Perceived mastery goals structure in Junior High was negatively related to biased preferences for cooperation partners, and perceived performance goals structure in Junior High was positively related to these biased preferences, over and beyond prior biased preferences for cooperation partners, achievement goal structure, personal achievement goals, and academic efficacy assessed in elementary school. These relations were found also after controlling for students’ preferences for cooperating with peers with similar level of academic ability, thus providing support to hypotheses concerning the social identity processes that are triggered by academic achievement goal structure.