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Soil borne archaea in agricultural systems is crucial for cycling of nutrient such as Nitrogen, Carbon and Sulphur. The objective of the study was to assess the effect of different tillage systems on functional archaea diversity in a 15 years cereal-legume rotation field using Illumina sequencing platform for archaea 16S rRNA gene. The treatments in the study included conventional tillage with stubble removed (T), no-till with stubble removed (NT), conventional tillage with stubble incorporated (TS) and no-till with stubble retained (NTS). The results showed that the dominant soil archaea phyla was Crenarchaeota (> 96%), followed by Euryarchaeota with a lower abundance of < 3% and then Parvarchaeota and other bacteria phyla made up < 1% across the treatments and depths. The treatment means were ranked as NT > NTS > TS > T for 16S rRNA number of OTUs, Shannon and Simpson indices calculated for the 0-10cm soil depth. Analysis of factor effect revealed that tillage but not stubble retention or their interaction significantly influenced (P < 0.01 and P < 0.05) 16S rRNA diversity. Non metric Multidimensional Scaling (NMDS) analysis clearly grouped the microbial communities according to depths. Linear Discriminant Analysis Effect Size (LEfSe) identified Crenarchaeota and Thaumarchaeota (to genus level) as significantly enriched clades in 0-10 cm depth of T while Euryarchaeota and Thermoplasmata were significantly enriched in TS. The conservational tillage systems (NT and NTS) promoted even distribution of archaea diversity while conventional tillage systems (T and TS) enriched the archaea communities identified in the study.