In light of climate change, the ability to predict evolutionary responses to temperature changes is of central importance for conservation efforts. Studying parallel evolution in natural populations inhabiting contrasting thermal environments presents a powerful approach for understanding and predicting responses to increasing temperatures. In this study, we used a natural experiment in Iceland, where freshwater populations of threespine sticklebacks are found in waters warmed by geothermal activity, adjacent to populations in ambient-temperature water bodies. We used three sympatric and three allopatric warm-cold population pairs to test for morphological divergence in relation to thermal habitat. We found that thermal habitat explained over 50% of body shape variation: fish from warm habitats had a deeper mid-body, a shorter jaw, smaller eyes, and longer dorsal spines. Population age did not influence the magnitude or direction of morphological divergence between warm and cold habitats. However, the absence of gene flow seemed to facilitate parallel evolution across thermal habitats: all three allopatric population pairs were on a common evolutionary trajectory, but this was not the case for sympatric population pairs. Our findings therefore suggest that morphological evolution in response to rising temperatures can be predictable to some extent but only if there is restricted gene flow.