Phenotypes manifest a balance between the inherited tendency to remain the same (phenotypic stability) and the tendency to change in response to current environmental conditions (adaptation). This paper explores the role of functional integration and functional trade-offs in generating phenotypic stability by limiting the responses of individual characters to environmental selection. Evolutionarily stable configurations (ESCs) are systems of functionally interacting characters within which characters are “judged” by their contribution to system-level functionality. This “internal” component of selection differs from traditional “external” selection in that it travels with the organism wherever it goes and is maintained across a wide range of environments. External selection, in contrast, is by definition environment-dependent. The temporal and geographic constancy of internal selection therefore acts to maintain phenotypic stability even as environments change. Functional trade-offs occur when one character participates in more than one function, but can only be optimized for one. Participation of certain (“keystone”) characters in a trade-off potentially causes stabilization of an entire system owing to a cascade of functional dependencies on that character. Phylogenetic character analysis is an essential part of elucidating these processes, but patterns cannot be used as prima facie evidence of particular processes.