The study aimed to extend current research on conditions that better support analogical encoding through mutual alignment. We focused on two variables that have not been examined independently in previous studies: the joint presentations of two cases of a scientific phenomenon and the explicit instructions for comparison. One hundred and sixty-five 5th graders and one hundred and sixty-eight 7th graders were presented with two pairs of scenarios, one about heat flow and the other about the state change of matter. Participants were randomly assigned to three conditions: sequential presentation of scenarios, joint presentation of scenarios and joint presentation of scenarios with explicit instructions to compare analogically. Results show that for both pairs of scenarios, analogical encoding was promoted more in the condition of joint presentation of scenarios with instructions for comparison. In addition, 7th graders benefited more from this condition than 5th graders.