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Abstract Multiple disturbances can have mixed effects on biodiversity. Whether the interaction of sequential disturbances drives local extinctions or promotes diversity depends on the severity of biomass reductions relative to any stabilizing and/or equalizing effects generated by the disturbance regimes.Through a manipulative mesocosm experiment, we examined how warming events in the fall and simulated grazing disturbance (i.e. clipping) in the winter affected the density, biomass and genotypic diversity of assemblages of the clonal seagrassZostera marina.We show that the interaction of the two disturbance types reduced density and biomass to a greater degree than warming or clipping alone.The genotype with the highest biomass in the assemblage shifted under the different experimental regimes such that the traits of winners were distinct in the different treatments. The favouring of different traits by different disturbances led to reduced evenness when a single disturbance was applied, and enhanced evenness under multiple disturbances.We conclude that sequential disturbances can alter the outcome of inter‐genotypic interactions and maintain genotypic diversity in clonal populations. Our study expands the context in which disturbance can influence intraspecific diversity by showing that fluctuating selection may result from the sequential application of different disturbance types and not simply seasonal changes in a single agent. A freePlain Language Summarycan be found within the Supporting Information of this article.