Abstract: As the main methods of the second generation high-throughput sequencing technologies, 454 pyrosequencing and Illumina sequencing have been widely utilized in the microbial nucleic acid analysis.In this study, sequence length, microbial compositions, abundance and diversity in the sediments from the adjacent area of Yangtze Estuary were analyzed using 16S rRNA gene-based 454 pyrosequencing and Illumina sequencing technology to compare the advantages and disadvantages of two techniques.The results showed that more sequences and OTUs were obtained by Illumina sequencing, which included many rare species.Illumina sequencing technology had an advantage of microbiological community analysis over 454 pyrosequencing technology, especially in the detection of rare species.In summary, Illumina sequencing technology was better than 454 pyrosequencing technology in the analysis of microbial diversity and community composition.454 pyrosequencing didn't reflect its advantage in long read length, and it probably underestimated the microbial composition and diversity.