AimAtolls are a widely distributed, common type of tropical ecosystem, each consisting of an annular coral reef and up to several hundred individual islets sitting on the reef platform. The small land areas and low elevation render the terrestrial communities susceptible to local extinctions from overwash and inundation due to tropical cyclones. Such recurring catastrophic disturbances should be expected to drive strong priority effects and historical contingency in species assembly, thus also promoting species turnover within atolls. This stands contradictory to the received wisdom of atolls consisting of numerous uniform, replicated island systems. We tested the hypothesis that the individual islets within an atoll exhibit compositional turnover and that this species turnover within atolls is related to cyclone frequency.LocationAtolls worldwide.Time PeriodPresent.Taxa StudiedVascular plants, reptiles, birds.MethodsWe compiled a global dataset at the level of islets for species presence/absence within atolls. We obtained long‐term (80 year) tropical cyclone frequency data for each atoll from the NOAA hurricane database and used Bayesian regression to estimate the effects of tropical cyclone frequency on species turnover within atolls.ResultsWe consistently measured high within‐atoll species turnover (i.e., between the individual islets within an atoll) on atolls worldwide. The degree of within‐atoll species turnover increases with increasing tropical cyclone frequency. Atolls that are more frequently hit by tropical cyclones show higher species turnover between their islets than those that occur outside the tropical cyclone belt.Main ConclusionsTropical cyclones are a significant driver of the community assemblages on atolls. These catastrophic disturbances promote a heterogenous atoll landscape, which challenges perceptions that the islets within an atoll are identical replicates of the entire atoll terrestrial community. Biodiversity surveys undertaken at the islet‐level (alpha‐diversity) might therefore not be representative of the entire atoll metacommunity (gamma) diversity.