The lacertid lizard (Gallotia stehlini), an endemic of Gran Canaria, shows no visually obvious geographic variation, yet all seven scalation characters that were examined exhibit significant geographic variation. The number of collar scales, scales along the ventral trunk and femoral pores are correlated with habitat type, while the number of femoral pores is correlated negatively with altitude. Mantel tests were used to compare simultaneously an observed pattern with three hypothesized patterns (habitat type, altitude and proximity). They indicate that, while several individual characters are significantly associated with the putative causal factors of habitat type and altitude, there is no association between an overall scalation distance matrix and habitat type, or altitude when the effect of proximity is removed. Consequently, one should consider the individual characters as well as the multivariate generalized distances. Some of the observed patterns of geographic variation in scalation are very similar to those of the small scincid lizardChalcides sexlineatuson Gran Canaria and also parallel the altitudinal and latitudinal variation in the scalation of the Tenerife lacertid (Galotia galloti). The low level of congruence in patterns of geographic variation in individual characters (i.e. some vary with latitude, some with altitude and one varies with longitude) is consistent with the hypothesis that ecogenetically caused geographic variation may result in lower inter‐character congruence than phylogenetically caused geographic variatio