Aim The role that geography plays in promoting speciation by spatially isolating populations has been studied extensively, but less attention has been devoted to assessing the role of isolation by time mediated by spatial variation in climate as a mechanism promoting population divergence. Gene flow between populations differing in their reproductive schedules might be reduced relative to that between populations with overlapping breeding seasons, potentially leading to genetic divergence. Assuming that precipitation influences reproductive schedules, we explored the effect of asynchronous precipitation regimes on intraspecific genetic divergence. In addition, we examined whether microevolutionary processes are reflected in macroevolutionary patterns by assessing whether regions with more asynchronous precipitation across space have higher frog species richness and have experienced greater speciation rates than regions with more spatially synchronous precipitation regimes. Location Central and South America. Taxon Anurans: across 38 species of Neotropical frogs. Methods For microevolutionary analyses, we assessed the relationship between spatial asynchrony in precipitation and mitochondrial DNA genetic divergence accounting for ecological connectivity using multiple regression and phylogenetic meta‐analyses. For macroevolutionary analyses, we assessed the relationship between species richness, speciation rates estimated from a comprehensive molecular phylogeny, and the degree of spatial asynchrony in precipitation using generalized linear models. Results We found that spatial asynchrony in precipitation is positively associated with genetic differentiation in 39% of the species tested, resulting in a weak cross‐species effect. However, the effect of asynchrony in precipitation on population divergence seems not to scale to macroevolutionary patterns because spatial asynchrony in precipitation was not associated with geographical patterns of species richness nor speciation rates. Main Conclusions Our results indicate that asynchronous breeding may promote genetic divergence even in the absence of geographical barriers in species where breeding is associated with water availability, but such effects may not be stable enough through time to influence macroevolutionary patterns.