Using functional magnetic resonance imaging (fMRI), this study investigates and discusses neurological explanations for, and the educational implications of, the neural network activations involved in hypothesis-generating and hypothesis-understanding for biology education. Two sets of task paradigms about biological phenomena were designed: hypothesis-generating and hypothesis-understanding, and 60 healthy participants performed the tasks. fMRI results showed that participants utilised different neural networks during hypothesis-generating and hypothesis-understanding, and these networks appeared to have specialised patterns. In other words, these two types of learning strategies related to hypotheses do not share the same brain region or network. Therefore, for biology learning, it might be concluded that hypothesis-generating and hypothesis-understanding are operating at differing neural network levels, which causes the difficulty students have generating hypotheses about complicated natural phenomena despite a huge amount of exposure to hypothesis-understanding during their learning. (Contains 3 figures and 2 tables.)