Relocation of endangered species can be an effective conservation tool if it does not mix populations that represent significant intraspecific variation. The threatened Italian agile frog, Rana latastei, has small populations with low genetic diversity: translocation has been proposed to improve the likelihood of survival of populations. Using a common environment experiment and field surveys, we investigated whether there were differences in larval growth and developmental rate between foothill and lowland R. latastei populations, to evaluate if they are evolutionarily significant units. In nature, the colder climate of the foothills causes delayed metamorphosis. Conversely, in a common environment, larvae from foothill populations show faster growth and development. We did not find a significant egg-size related maternal effect or any differences in size at metamorphosis. We hypothesise that counter-gradient selection promoted fast growing phenotypes in a cold environment, where low temperatures slow down larval development. Foothill populations, despite being only a small geographical distance away from lowland populations, seem to be adapted to a colder climate and represent an evolutionarily significant unit. Different populations should, therefore, be managed independently, avoiding translocation. We suggest that evolutionary divergence between populations should be verified prior to planning relocation programmes, to prevent the risk of genetic homogenisation.