The evolution of biological systems is influenced by a number of factors and forces that have acted in different combinations at different times to give rise to extant organisms. Here we illustrate some of the issues surrounding the data-driven evolutionary analysis of biological systems in the context of bacterial two-component systems (TCSs). TCSs are critical for bacteria to interact with their extracellular environment. A typical TCS consists of a histidine kinase on the membrane and a response regulator in the cytoplasm. Here we comprehensively characterise the extent to which these appear together across some 950 bacterial species and test for statistically significant patterns of correlated gain and loss. Our analysis provides evidence for correlated evolution but also a high level of evolutionary flexibility: at the sequence level, histidine kinases but especially response regulators belonging to different TCSs in a species show high levels of similarity, which may facilitate crosstalk as well as the recruitment of components into new compound signalling systems. We furthermore find that bacterial lifestyle has an overriding influence on the presence and absence of TCS; while in most TCSs either both or none of the two components are present, several TCSs tend to lose preferentially either the histidine kinase or response regulator component, which further supports the notion of reuse and reshuffling of these components in different TCS arrangements. We conclude by placing these findings in a wider context and discuss the implications for evolutionary systems biology more generally.