Plants harbor complex and variable microbial communities. Using molecular-based techniques targeting the 16S rRNA gene, we studied the developmental stages and geographical location diversity of endophytic archaea in two locations (Shihezi and Changji) and four periods (the seedling growth, rosette formation, tuber growth and sucrose accumulation sampling periods) in the north slope of Tianshan Mountain, China. Community structure of mixed sample from 60 sugar beet plants was examined using PCR-based 454 pyrosequencing and terminal restriction fragment length polymorphism (T-RFLP). In total, 5290 archaea 16S rRNA sequences were obtained from all sugar beet samples. The most abundant archaea groups in all sugar beet were Methanococci, the miscellaneous Crenarchaeotic Group and Thermoplasmata. There was a marked difference in diversity of endophytic archaea in sugar beet for different growth periods. The greatest number of Operational T-RFLP Units (OTUs) was detected during sucrose accumulation (298) and rosette formation (282). Endophytic archaea diversity was reduced during seedling growth (128 OTUs) and tuber growth (55 OTUs). Nine OTUs were common to all four periods of growth. There were more OTUs in Shihezi than in Changji. Clustering analysis and principal component analysis of T-RFLP data revealed distinct shifts in endophytic archaea community profiles that corresponded to plant growth stage rather than geographical location. The dynamics of endophytic archaea communities were influenced by plant growth stage. To our knowledge, this is the first report that archaea has been identified as endophytes associated with sugar beet by the culture-independent approach. The results suggest that the diversity of endophytic archaea is abundant in sugar beet.