AbstractAimSpecies richness varies widely across space and is determined by underlying factors that drive species coexistence. Such factors include the speciation process (sympatric vs. allopatric), time since divergence, geographic context and intrinsic properties of the organisms. We model for the first time the coexistence dynamics of lizards and snakes across broad temporal and spatial scales, investigating whether an increase in niche divergence, dispersal abilities and inhabiting islands or continents affect their probability of coexistence.LocationGlobal.Time periodCenozoic.Major taxa studiedSquamata.MethodsWe used 447 sister species pairs, their age since divergence, their level of spatial (sympatric or allopatric) and niche overlap and geographical setting (islands or continents) to fit probabilistic models of species coexistence. We measured morphological traits to quantify niche divergence and used range and body size as proxies for dispersal ability. We applied a model‐comparison framework in lizards and snakes separately to evaluate which factors best explained their coexistence dynamics.ResultsAllopatric speciation is the main speciation mode in snakes but we did not find evidence to favour one speciation mode in lizards. In snakes, sympatric pairs tend to occur on islands and to be more different in body size. On the contrary, dispersal ability shaped the coexistence of lizards, where species were more likely to coexist when they have higher dispersal abilities.Main conclusionsDistinct patterns and mechanisms underlie species coexistence within the order Squamata. Snake coexistence is preferentially produced by secondary sympatry favoured by niche divergence and is more likely to occur in more restricted geographical settings (islands vs. continents). Coexistence in lizards is strongly influenced only by dispersal abilities, but the high heterogeneity of processes simultaneously shaping the distribution of different lizard lineages might have masked specific coexistence signals, and future work should compare coexistence dynamics between clades (e.g. families).