This qualitative study based on Gee’s (2001) identity theory examined and compared how American and Chinese middle school students develop identities towards science, culture and technology in an intercultural web-assisted scientific inquiry project. Through analysis of online discussions, videoconferences, interviews, surveys and fieldnotes, we explored how students shaped and reshaped their identities throughout scientific inquiry learning and intercultural collaborative activities. In examining identity development during scientific investigation, we offer insights into the intercultural learning context and suggest ways of facilitating identity formation, which can inform such collaborations in the future.