The protection and restoration of mangrove ecosystems depend on understanding the interaction between benthic organisms and mangrove succession. Although benthic protozoa are important in such ecosystems, protozoan community dynamics have seldom been studied during the mangrove succession. The benthic protozoa of a mangrove chronosequence that included a primary community (unvegetated shoal), an early community (Avicennia marina), a middle community (Aegiceras corniculatum), and a late community (Bruguiera gymnorrhiza + Rhizophora stylosa) were investigated to determine the changes in the benthic protozoan community during a mangrove succession at Zhanjiang, China. A total of 62 benthic protozoa taxa belonging to three classes, 26 orders, and 38 families were recorded. The abundance of benthic protozoa decreased significantly during mangrove succession, while species richness and diversity changed irregularly. Hierarchical clustering indicated that the distribution of the benthic protozoa closely corresponded with the mangrove successional stages. Further analyses indicated that the changes in the benthic protozoan community with mangrove succession were associated with the changes in total sediment nitrogen content and especially with vegetation characteristics, including plant height and crown breadth. The decline in the abundance of benthic protozoa during mangrove succession may be explained by the deterioration of benthic protozoan microhabitats. However, determining whether these or other factors are responsible for the change in the benthic protozoan community during mangrove succession will require additional research.