Two hypotheses about theoretical concept acquisition, application, and change were tested. College biology students classified as intuitive, transitional, or reflective (hypothetico-deductive) reasoners were first taught two theoretical concepts (molecular polarity and bonding) to explain the mixing of dye with water, but not with oil, when all three were shaken in a container. The students were then tested in a context in which they misapplied the concepts in an attempt to explain the gradual spread of blue dye in standing water. Next students were taught another theoretical concept (diffusion), with and without the use of physical analogues. They were retested to see which students acquired the concept of diffusion and which students changed from use of the incorrect polarity and bonding concepts (i.e., the misconceptions) to use of the diffusion concept to correctly explain the dye's gradual spread. As predicted, the experimental/analogy group scored significantly higher than the control group on a posttest question that required the definition of diffusion. Also as predicted, hypothetico-deductive reasoning skill was significantly related to correct application of the diffusion concept and to a change from the misapplication of the polarity and bonding concepts to the correct application of the diffusion concept to explain the gradual spread of the blue dye. Thus, the results support the hypotheses that physical analogues are helpful in theoretical concept acquisition and that hypothetico-deductive reasoning is needed for successful concept application and change. Educational implications are drawn.