When she was in the Resistance's village, she remembered having a conversation with Rodolphus the first night he appeared to her in his animagus form. He claimed that only Ginny and Aberforth Dumbledore knew who he actually was. She couldn't imagine that Aberforth would be the spy, not after he'd been so angry with her when she told him that she didn't want to spy for the Resistance. That only left Ginny. She hated to think that was true, but after learning what other secrets she was capable of keeping, Hermione couldn't discount the possibility.