This study analyzed the spatio-temporal patterns of 4,587 (94% of the total) confirmed dengue cases in Kaohsiung and Fengshan Cities (a two-city area) that occurred in Taiwan from 2001 to 2003. The epidemic had two simultaneous distinct diffusion patterns. One was a contiguous pattern, mostly limited to 1 km from an initial cluster, reflecting that there was a rapid dispersal of infected Aedes aegypti and viremic persons. The second followed a relocation pattern, involving clusters of cases that diffused over 10 weeks starting from the southern and moving to the northern parts of the two-city area. The virus from one clustering site jumped to several distant areas where it rapidly dispersed through a series of human-mosquito transmission cycles to several localities. In both patterns, transmission of disease quickly enlarged the epidemic areas. Future dengue control efforts would benefit from a timely syndromic surveillance system plus extensive public education on how to avoid further transmission.