Understanding many scientific phenomena, processes, or systems may be especially dependent on a student's ability to visualize or manipulate spatial information in order to construct mental representations. One instructional technique often included in science texts to help students to understand difficult concepts is the use of concrete or familiar analogies. Two experiments tested whether individual differences in spatial skills may impact the effectiveness of learning by analogy, if an analogy might particularly improve the learning of low-spatial students, and if the way in which the analogical comparison is presented matters. In these studies, students read a text about the processes and causes of the global weather phenomenon known as El Niño. For some students, the text also contained an analogy that compared El Niño to the inflating a deflating of a balloon; this analogy was either presented at the beginning of the text or interleaved throughout the text. Across both experiments, results indicated that spatial skills generally improved learning from a text about El Niño, but that interleaving an analogy changed the relationship between spatial skills and learning, and improved performance for low-spatial learners.