Geometric morphometrics, the science about the study of shape,has developed much in the last twenty years. In this thesis I firststudy the reliability of the phylogenies built using geometricmorphometrics. The effect of different evolutionary models,branch-length combinations, dimensionality and degrees ofintegration is explored using computer simulations.Unfortunately in the most common situations (presence ofstabilizing selection, short distance between internal nodes andpresence of integration) the reliability of the phylogenies is verylow. Different empirical studies are analysed to estimate thedegree of evolutionary integration usually found in nature. Thisgives an idea about how powerful the effect of integration is overthe reliability of the phylogenies in empirical studies.Evolutionary integration is studied looking at the decrease ofvariance in the principal components of the tangent shape spaceusing the independent contrasts of shape. The results suggestthat empirical data usually show strong degrees of integration inmost of the organisms and structures analysed. These are badnews, since strong degree of integration has devastating effectsover the phylogenetic reliability, as suggested by oursimulations. However, we also propose the existence of othertheoretical situations in which strong integration may nottranslate into convergence between species, like perpendicularorientation of the integration patterns or big total variancerelative to the distance between species in the shape space.Finally, geometric morphometrics is applied to the study of theevolution of shape in proteins. There are reasons to think that,because of their modular nature and huge dimensionality,proteins may show different patterns of evolutionary integration.Unfortunately, proteins also show strong functional demands,which influence their evolution and that cause strong integrationpatterns. Integration is then confirmed as a widespread propertyin the evolution of shape, which causes poor phylogeneticestimates.