The microeukaryotic community structure and response to indoor simulated bioremediation by Nereis succinea of mudflat sediments in Jimei, Xiamen, was investigated by PCR-DGGE. The results indicated that the microeukaryotes in mudflat sediments of Jimei were mainly divided into four groups: Metazoa (including 6 phyla: Gnathostomulida, Annelida, Nematoda, Arthropoda, Mollusca and Gastrotricha), Cercozoa, Bacillariophyta and Alveolata (including Pyrrophyta and Ciliophora). The dominant group was Ciliophora, and the subdominant group was Nematoda. Peridinium quinquecorne (belonging to Pyrrophyta) was the dominant species. Cluster analysis of DGGE profiles indicated that nereids bioturbation had influenced the microeukaryotic community, and the treatment samples with nereids clustered together and separated from the control samples without N. succinea. More Nematoda were detected in treatment samples, which probably indicated that the nereid bioturbation stimulated the growth of Nematoda.