Phenotypic integration, defined as the coordinated co-variation of parts of an organism can be an important constraint on phenotypic diversification. Functional factors, by having an heterogeneous impact across the animal body, may reinforce the integration of some parts while causing a perturbation of the integration among other parts. The integration across the locomotor apparatus should thus reflect to a certain extent the locomotor ecology of the animal. Using the mustelids as study group, we track changes in the patterns of co-variation in species belonging to four different locomotor ecologies (terrestrial, semi-arboreal, semi-fossorial, and semi-aquatic). Our results highlight the strong overall integration in mustelid long bones. The main shape changes associated with co-variations between skeletal elements are the bone robustness and proportions of the epiphyses. The pattern of co-variation is, however, only slightly impacted by allometry. Changes in co-variation between species mostly scale with phylogenetic divergence time, except for the (Mustela putorius, M. eversmanni, M. lutreola) clade which, despite a short divergence time, presents strong differences in co-variation. Co-variation patterns differ between locomotor ecologies, but few of these variations match the hypothesis of a reduction of integration due to functional specialization. This may reflect our lack of knowledge on the functional modules in species with locomotor ecologies that differ from terrestrial locomotion rather than invalidate our a priori hypotheses.