A particular threat posed by climate change for biodiversity conservation, one which has scarcely been studied, is the overlap of the potential distribution areas in phylogenetically closely related species. In this study, Species Distribution Modelling (SDM) was used to investigate the potential changes in the distribution of Delphinium bolosii and D. fissum subsp. sordidum under future climatic scenarios. These two closely related and endangered endemic species from the Iberian Peninsula do not have complete reproductive barriers between them. The two models selected different predictors with a similar effect in the biological cycle. Both taxa need low winter temperatures to break seed dormancy and sufficient rainfall to complete the flowering and fruiting stages. The current potential distribution areas of both taxa do not currently overlap. However, the results showed that potential changes may take place in the species’ distribution range under future climate scenarios. The models predict a reduction of the potential distribution area of D. bolosii while, conversely, the potential distribution area of D. fissum subsp. sordidum increased. In both cases, the predicted contraction in range is very high, and loss of habitat suitability in some current localities is worrying. Notwithstanding, the models do not predict overlaps of potential areas under climate change scenarios. Our findings can be used to define areas and populations of high priority for conservation or to take action against the impacts of climate change on these endangered species.