Soil and plant microbiota are playing an eminent role in shaping both natural ecosystems and agricultural production systems. It is now widely admitted that bacterial communities show a great diversity in both the plant rhizosphere and the plant endosphere. These microbial communities affect the fitness of the hosts and further play important roles in C and N cycles. While bacterial communities have been widely studied, much less is known about archaeal communities and the role they play within the rhizosphere and the endosphere. The objective of our study was to develop a multigenic metabarcoding approach to accurately describe the diversity of archaeal communities interacting with rice paddies in the Rhône delta region. This pilot agro-ecosystem was selected because it is annually subjected to several abiotic stresses (water stress associated to rice paddies flooding, soil salinity, high production of methane, etc.) that are likely to enhance archaeal growth. We used archaeal specific primers within the universal 16S rRNA gene and the mcrA gene (encoding the methyl-coenzyme M reductase subunit A of methanogens). An evaluation of the efficiency of the primers was carried out on mock cultures and plant samples. Two rice-compartments during both rice paddies flooding and drying periods were collected and analyzed. This study is likely to be a first step towards better describing rice-associated archaeal communities and understanding the dynamics of these communities in relation with abiotic constraints of rice paddies in Camargue.