A research of microbial diversity in ballast water sediments was conducted by using Illumina MiSeq2500 high-throughput sequencing analysis. The bacterial samples of ballast water sediment which were sampled from eleven international ships anchoring at Shanghai Port were sequenced and the biological diversity and community structure was analyzed. Total 420,069 of valid reads from 11 samples were obtained, including 38 phyla, 98classes, 226 orders, 393 Families and 704 Genera. The dominant groups were Proteobacteria (72.98%), Actinobacteria (9.11%),Bacteroidetes (8.71%), Chloroflexi (4.06%), Gemmatimonadetes (1.47%), Acidobacteria (1.18%),and others (2.50%). The pathogenic bacteria were also discovered such as Mycobacterium, Planococcus, Paenibacillus, Streptomyces and Inquilinus. The result shows that there are abundant microbes in ballast water sediments. Our study is the first step of having a comprehensive understanding of microorganism in ballast sediment from the ships in a Chinese port and it lays the foundation for researching the invasion mechanism from ballast water.