The modular organization of tetrapod paired limbs and girdles, influenced by the expression of Hox genes is one of the primary driving forces of the evolution of animal locomotion. The increased morphological diversification of the paired limbs is correlated with reduced between-limb covariation, while correlation within the elements is usually higher than between the elements. The tailed amphibians, such as Lissotriton newts, have a biphasic lifestyle with aquatic and terrestrial environments imposing different constraints on limb skeleton. By employing the methods of computerized microtomography and 3D geometric morphometrics, we explored the pattern of morphological variation, disparity, modularity and morphological integration in the proximal parts of the anterior limbs of six species of Eurasian small bodied newts. Although the species significantly differ in limb shape, there is a great overlap in morphology of scapula and humerus, and there are no differences in morphological disparity. For the scapula, the shape differences related to the duration of the aquatic period are in length, depth and curvature. The shape of the humerus is not affected by the length of aquatic period, and shape differences between the species are related to robustness of the body. The length of aquatic period has statistically supported phylogenetic signal. The scapula and humerus are structures of varying modularity. For the humerus, the strongest support on the phylogenetic level was for the capitulum/shaft hypothesis, which can also be interpreted as functional modularity. For the scapula, the greatest support was for the antero-posterior hypothesis of modularity in case of Lissotriton vulgaris, which can be explained by different functional roles and muscle insertion patterns, while there was no phylogenetic modularity. The modularity patterns seem to correspond with the general tetrapod pattern, with modularity being more pronounced in the distal structure. The future research should include more salamandrid taxa with different habitat preferences and both adult and larval stages, in order to explore how size, phylogeny and ecology affect the morphology and covariation patterns of limbs.