We investigated the diel cycle mechanism of a tide-pool ciliate community of the northeastern coast of Taiwan. The investigation was conducted on 17th-18th June (typical summer weather), and on 23th-24th July 2013 (10 days after a typhoon). In June, the tide-pool ecosystem was an independent and the excystment of ciliates in the tide-pool caused a dramatic increase in population abundance, as well as composition change. In July, there was no significant difference between the species composition in the tide-pool and that in the surrounding coastal water. However, the abundance of ciliates in the tide-pool was lower due to the inability of ciliates to adapt to the tide-pool environment. From these results, we infer that the excystment of ciliates plays an important role in the diel cycle of the ciliate population in a tide-pool.