The bacterial community in a historic lake sediment core of Ardley Island, Antarctica, spanning approximately 1,600 years, was investigated by molecular approaches targeting the 16S rRNA gene fragments. The cell number in each 1 cm layer of the sediment core was deduced through semi-quantification of the 16S rRNA gene copies by quantitative competitive PCR (QC-PCR). It was found that the total bacterial numbers remained relatively stable along the entire 59 cm sediment core. Denaturing Gradient Gel Electrophoresis (DGGE) analysis and sequencing of PCR-amplified 16S rRNA gene fragments were performed to analyze the bacterial diversity over the entire column. Principle coordinates analysis suggested that the bacterial communities along the sediment core could be separated into three groups. There were obvious bacterial community shift among groups of 1-20 cm, 21-46 cm and 46-59 cm. Diversity indices indicated that the bacterial community in the 21-46 cm depth showed the highest species diversity and uniformity. The main bacterial groups in the sediments fell into 4 major lineages of the gram-negative bacteria: the alpha, gamma and delta subdivision of Proteobacteria, the Cytophaga-Flavobacteria-Bacteroides, and some unknown sequences. The gram-positive bacteria Gemmatimonadetes, Firmicutes and Actinobacteria were also detected. The results demonstrated the presence of highly diverse bacterial community population in the Antarctic lake sediment core. And the possible influence of climate and penguin population change on the bacterial community shift along the sediment core was discussed.