Abstract Podarcis dugesii is a polymorphic species found on the ecologically‐heterogeneous Atlantic island of Madeira. Patterns of geographic variation in size‐free body dimensions (body shape), scalation, and size were portrayed on maps with isophene contours. There was no dominant pattern of among‐site variation as seen in several other island lizards, although some linear combinations of morphological variables showed evidence of clines towards the east coast. Multivariate statistical techniques were developed to evaluate whether morphological variation contained an ecology‐related spatial pattern, after removal of the effects of statistical non‐independence of studied populations. Specifically, a partial correlation matrix comparison method provided evidence to support a proposed elevation model of among‐site divergence in scalation and body size, with both an alternative rainfall model and spatial non‐independence held constant. Similar divergence in scalation has been observed in other lizard species on other island archipelagos as well on some continental areas. The rainfall model was rejected for both body shape and scalation. The degree of within‐population polymorphism in body shape and scalation showed no clear geographic trends in general, although the elevation and rainfall models could not be rejected for female scalation.