The sequence in which disturbance events occur has the potential to affect the structure of ecological communities, but its role has been generally overlooked. Most disturbance studies have focused on the frequency or intensity of disturbance, probably reflecting the influence of the intermediate disturbance hypothesis. To investigate the effects of disturbance sequence on community structure, I created laboratory microcosms of protists and small metazoans analogous to communities found in water-filled bamboo stumps. Using drought (disturbance D) and larval mosquito addition (disturbance M), I examined the following five treatments of disturbance sequence: D-M-D-M, D-D-M-M, M-D-M-D, M-M-D-D, and no disturbance as a control. The response of species to disturbance varied between disturbance types (D or M) as well as among species, and disturbance effects depended on previous disturbance events. As a result, disturbance sequence drove the microcosms onto different successional trajectories, sometimes leading to divergence in final community states in terms of species richness or species composition and relative abundance. This divergence occurred even under the same frequency and intensity of disturbance. These results suggest that historical information on disturbance sequence can be essential for explaining variation in community structure. The interaction of sequence with frequency and intensity likely enhances the role played by disturbance in ecological communities.