Archaea was distributed widely in marine environments. It plays an important role in nutrient and energy cycling in marine ecosystems. For studying the archaeal spatial distribution in sediment of cage culture area, archaeal community structures in sediments were investigated in July 2011, in Xiangshan Bay, Zhejiang Province, China. Sediments used in this paper were as the same as described previously^[1]: a control or check site (CK), an intersection site 6-8 km from the aquaculture site (IS), and a cage culture site (AC). For sub-sampling, sediments were cut into several sections throughout their depth: a (0-5 cm), b (5-10 cm), c (10-15 cm), d (15-20 cm), e (20-25 cm) and f (50-55 cm). Physiochemical factors (NH₄⁺, NO₂^-, NO₃^-, SiO₃^2- and P) of sediments were analyzed in laboratory after transport with liquid nitrogen. Based on 16S rRNA gene, the structure and diversity of archaeal communities in sediments were analyzed by T-RFLP (Terminal Restriction Fragment Length Polymorphism), which was conducted after amplification of the archaeal 16S rRNA partial gene using a fluorescent primer pair 109F /934R-FAM and digestion by TaqI (T^CGA). Archaeal 16S rRNA gene clone library was constructed using DNA extracted from layer 0-5 cm sediment of the CK site, and the following phylogenetic analysis was carried out using ARB software. In agreement with other studies, Crenarchaeota is the dominant archaea in marine sediment. T-RFLP profiles showed that the dominant T-RF of 188 bp, affiliated to Crenarchaeota, occupied 80.3% in the cage culture site, more than it in the check site (61.2%). While, the kingdoms Euryarchaeota and Crenarchaeota were present equally in clone library and methanogens constituted a small proportion of the archaeal community. Because the check site is near to East Sea with a higher salinity, T-RF of 78 bp, belonged Halobacteriales, emerged in its upper layers (0-20 cm) sediments and was more abundant than it in other sites. Principal component analysis for the archaeal 16S rRNA gene T-RFLP using R software indicated a complete separation of archaeal communities of the cage culture sit from the check site. And archaeal communities of the intersection site were in the middle. An obvious difference of archaeal communities in the check site sediments at various depths was indicated by PCA. T-RFs of 78 bp, 88 bp, 383 bp and 188 bp related archaea may be the main microorganisms who made the difference among horizontal and vertical distribution. Although calculation of Shannon diversity index H' and evenness index E' showed large errors in parallels, comparing with the check site, the diversity of archaeal communities in cage culture sediments displayed a dropping tendency. Redundancy analysis of archaeal community compositions and environmental factors of sediments in different sites and depths suggested that nutritive salt and pH mainly affected the distribution of archaeal in horizontal by aquaculture. Eh and ammonium were tend to have a relation with archaeal vertical distribution, especially in the check site. In short, aquaculture affected the spatial distribution of uncultivated archaea.