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Aim: When modelling future or past geographic distributions of a species, attention should be paid to the possible differentiated responses to climate changes between lineages. Dispersal also plays an important role in the capacity of species to track suitable climate, which is particularly relevant for amphibians with limited dispersal ability. In this study, we included different lineages and dispersal distances into species distribution models to make them more biologically relevant in face of climate change scenarios. Location: Europe. Taxa: Bombina variegata and its lineages. Methods: Using MaxEnt, we fitted correlative niche models for B. variegata lineages and also for the species level (B. variegata sensu lato) that we projected under Last Glacial Maximum (LGM) and future climate scenarios (RCP2.6, RCP8.5). A comparison of projections was conducted considering both unlimited and limited dispersal abilities. Results: We found that the B. variegata lineages differed in their bioclimatic niches. In general, models run without discriminating the lineages showed reduced suitable areas compared to models run at each lineage, especially those for B. variegata pachypus and B. variegata scabra (southern lineages). Suitable areas identified for the LGM match with the climatic refugia identified in phylogeographic studies. Projections for the mid‐Holocene showed the increase of suitable areas for the lineages B. variegata variegata "Carpathians" and "Western" while they decreased for the southern lineages. In the future (2040–2080), only models under limited dispersal predict the extinction of the Carpathian lineage and a reduction in suitable areas for the other lineages, regardless of periods and scenarios. Main conclusions: We demonstrated important shifts in habitat suitability in Europe suggesting range‐shifts about hundreds of kilometres in response to past climate changes. However, rapid and unprecedented changes in suitability are expected in the future due to the accelerated climate warming during the 21st. According to their limited dispersal abilities, the persistence of all B. variegata lineages over time appears uncertain. We further recommend to integrate the intraspecific levels, when available, in modelling process to catch local variations and obtain more accurate results. [ABSTRACT FROM AUTHOR]