Abstract Aim The patterns and causes of ecogeographical body size variation in ectotherms remain controversial. In amphibians, recent genetic studies are leading to the discovery of many cryptic species. We analysed the relationships between body size and climate for a salamander (Salamandrina) that was recently separated into two sibling species, to evaluate how ignoring interspecific and intraspecific genetic structure may affect the conclusions of ecogeographical studies. We also considered the potential effects of factors acting at a local scale. Location Thirty-four populations covering the whole range of Salamandrina, which is endemic to peninsular Italy. Methods We pooled original data and data from the literature to obtain information on the snout–vent length (SVL) of 3850 Salamandrina females; we obtained high-resolution climatic data from the sampled localities. We used an information-theoretic approach to evaluate the roles of climate, genetic features (mitochondrial haplogroup identity) and characteristics of aquatic oviposition sites. We repeated our analyses three times: in the first analysis we ignored genetic data on intraspecific and interspecific variation; in the second one we considered the recently discovered differences between the two sibling species; in the third one we included information on intraspecific genetic structure within Salamandrina perspicillata (for Salamandrina terdigitata the sample size was too small to perform intraspecific analyses). Results If genetic information was ignored, our analysis suggested the existence of a relationship between SVL and climatic variables, with populations of large body size in areas with high precipitation and high thermal range. If species identity was included in the analysis, the role of climatic features was much weaker. When intraspecific genetic differences were also considered, no climatic feature had an effect. In all analyses, local factors were important and explained a large proportion of the variation; populations spawning in still water had a larger body size. Main conclusions An imperfect knowledge of species boundaries, or overlooking the intraspecific genetic variation can strongly affect the results of analyses of body size variation. Furthermore, local factors can be more important than the large-scale parameters traditionally considered, particularly in species with a small range.