A combined analysis of nuclear, mitochondrial and morphological data robustly resolves snakes as the sister taxon to anguimorph ‘lizards’. Analysed in isolation, nuclear DNA (nDNA) produces a trichotomy between snakes, iguanians and anguimorphs, mitochondrial DNA (mtDNA) is largely uninformative at deeper levels, and morphology tends to nest snakes deep within anguimorphs or with various legless squamate groups. When analysed simultaneously, the nuclear signal is sufficiently strong that mtDNA and morphology are constrained to choose between alternative resolutions of the iguanian–anguimorph–snake trichotomy (generated by the nDNA) – and both support the snake–anguimorph solution. Combined analyses of fast-evolving or idiosyncratically evolving markers (mtNDA, morphology) with conservative traits (e.g. nuclear genes) might be the best way to resolve ancient, closely spaced divergences. Fast or idiosyncratic markers potentially provide the most information about short, ancient internodes, but can converge on spurious trees if analysed in isolation. However, if constrained to only choosing between plausible trees, such data can contribute unique and valuable phylogenetic signal that resolves such problematic divergences.