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There is no evidence to suggest that Rousseau does not recognize Ben Linus as the man who stole Alex. It may seem safe to assume that she does not recognize him because she does not share this information with Sayid, but we can't really make assumptions about Rouseau's thought-processes, given her lack of sanity. She does tell Sayid that she knows for a fact that Ben is "one of them," which indicates that she does recognize him. She also specifically selects Sayid as the person to whom to deliver Ben, which suggests to me that she not only remembers Ben, but dislikes him enough to believe Sayid should be the one to deal with him.

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