The Lataste's viper Vipera latastei is a medium-sized viper distributed throughout almost the entire Iberian Peninsula and north-west of Africa. Former morphological studies noted the existence of two subspecies, V. l. gaditana and V. l. latastei, as well as a full species, V. monticola, in the High Atlas, corresponding to the prior overall range described for V. latastei. However, some results remained unclear in these former studies, e.g. the specific status of the Medium Atlas populations, the intra-subspecific differences in V. l. gaditana and, the true status of some isolated populations of the northern range. For this reason, 45 morphological characters were analysed in 672 preserved specimens covering the entire range. Categorical Principal Components Analysis (CATPCA) and Discriminant Function Analysis (DFA) were used to assess geographic variability, treating specimens individually or assigning them a priori to groups, respectively. Geographic groups were established according to the origin of specimens in isolated areas of mountain chains. As the percentage of correct assignment was low in DFA, initial groups were combined to maximize the percentage. The results from the multivariate analysis suggest morphological differentiation between populations. Some variables accounted for geographic variability: e.g. rows of dorsal scales at mid-body are taxonomically stable and clearly separate the African populations; and number of ventral scales showed a clinal variation from 126 to 143 ventrals in extreme populations. The three African groups manifested clear morphological differences, and especially specimens from the High Atlas (V. monticola) and Alger. On the contrary, a large number of initial Iberian groups were merged because of the low scores in the correct classification. The final groups showed a vast central area with low morphological differentiation as well as isolated populations in the NW, NE and SW Iberian Peninsula. This conclusion matches well with allopatric speciation processes during the Quaternary ice ages, which contributed to the contraction/expansion of range, isolation events, and peripheral population refugia. Morphological differentiation in external characters of V. latastei exhibited similar results with respect to V. aspis and V. ammodytes, the vipers occupying other southern European peninsulas. Molecular markers will contribute to elucidate the relationships between V. latastei populations and the history of colonisation across the Strait of Gibraltar.