To better understand the role that fertilization systems play in soil fertility buildup and evolution, we employed denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) to determine the influence of different fertilization treatments on archaeal community structure in calcareous purplish paddy soil under rice/wheat rotations. The eight fertilization treatments were as follows: manure only (M), nitrogen plus manure (NM), nitrogen and phosphorus plus manure (NPM), nitrogen, phosphorus and potassium plus manure (NPKM), without fertilization (CK), mineral nitrogen (N), nitrogen-phosphorus (NP) and nitrogen, and phosphorus and potassium (NPK). Our results showed that long-term fertilization significantly affected soil archaeal community structure; the richness and diversity of archaeal community under NM, NP and NPKM were lower than those under the other fertilization treatments (M, NPM, CK, N, and NPK). Based on the DGGE patterns, two soil DNA samples isolated from the NPK-amended soil were used for RFLP analysis of archaea. Phylogenetic analyses showed that archaea in the calcareous purplish paddy soil was highly diverse, and the sequences were closely related to those archaeal sequences isolated from various soils and water environment. Cluster analysis of the DGGE profiles showed that archaeal communities under the eight fertilization treatments clustered into three groups. In soil from paddies currently under rice cultivation, the archaeal communities in the soil amended with M and NPK grouped into the first cluster, while NP was in the second group, and NPKM, NM, CK, N and NPM were in the third. In the soil with wheat cultivation, NP-treated archaeal communities clustered into a cluster, NPKM and M were in the second cluster, and N, NPK, NM, NPM and CK soil communities comprised the third cluster. The cluster analysis showed that crop type impacts the community structure of soil archaea.