The Sundarban mangroves are arguably the largest single stretch of contiguous mangrove forests in the world. They contribute immensely towards the maintenance of the global biogeochemical equilibrium along the shoreline of north-eastern India and the southern part of Bangladesh lying over the Bay of Bengal. They offer a unique microclimate and are also a highly productive ecosystem harboring diverse plants, animals, and microbial species. The resident microbial communities play an essential role in the maintenance of this ecosystem. Recent studies have shown that anthropogenic factors influence the diversity and distribution of microorganisms in the sediments of the Sundarban mangrove forests. Particularly, the distribution and diversity of resident archaeal communities in the sediment have been shown to be highly influenced by the level of pollutants (such as heavy metals and Polyaromatic hydrocarbons). In the present study, the DNA of the archaeal community associated with the rhizospheres of Ceriops decandra (locally known as Goran) and Avicennia officinalis (locally known as Bine), the two common native mangrove plants of Sundarban forest, was evaluated using 16S rRNA amplicon sequencing on an Illumina platform. The analysis revealed the overall dominance of Thaumarchaeota in the rhizosphere communities of both the plants (Goran and Bine) except for the rhizosphere communities of the Goran plants collected from sites with known anthropogenic disturbances. The phylum distribution pattern clearly demonstrated that the archaeal community structure of the rhizosphere of Goran plants from the sites under anthropogenic disturbance has an increased abundance of Euryarchaeota sequences. Interestingly, irrespective of the level of anthropogenic disturbances, the rhizosphere archaeal community pattern of the Bine plants was found to be similar. Besides Thaumarchaota and Euryarchaeota, there are a number of sequences affiliated to the following major phyla detected in the rhizosphere soils of both the mangrove plants: Bathyarchaeota, Lokiarchaeota, Marine Benthic Group E, Aenigmarchaeota, Hadesarchaea, Aigarchaeota, and Crenarchaeota AK8-group. Furthermore, we performed denaturing gradient gel electrophoresis (DGGE) to evaluate the influence of the anthropogenic factors on the nitrification, specifically aerobic ammonia oxidation mediated by ammonia-oxidizing archaea (AOA). Results indicated that AOA was abundant in all the rhizosphere soils analyzed. However, while the rhizosphere soils of Bine harbor a diverse AOA irrespective of the pollution status, Goran rhizosphere soils showed less AOA diversity, especially in the rhizosphere soils under high anthropogenic influences. Together, to the best of our knowledge, this is the first major analysis of mangrove rhizosphere archaeal communities in the backdrop of anthropogenic influences in the Sundarban forests. Moreover, the present study demonstrates that the influence of anthropogenic factors on the dynamics of rhizosphere archaeal communities is plant-specific.