A series of meromictic lakes exist along the northern coast of the island of Ellesmere in Nunavut (Canada). These highly laminated lakes have an ice cover that helps maintain the stability of salinity and temperature gradients in these ecosystems. The physical and chemical limnology of these polar lakes is well known. However, we know very little about the microbial populations they host. The aim of this work is to describe microbial diversity and environmental conditions in lakes so as to link the composition and function of communities to physico-chemical properties. The dissolved oxygen profile divides these aquatic ecosystems into three distinct water layers: an oxygen-rich area in the upper part of the lake, followed by a transitional zone and a deep anoxic zone. We sampled each of these three layers to take DNA samples to describe, using molecular tools (molecular cloning, quantitative PCR), the diversity and function of Archaea communities in two Arctic meromictic lakes (A and Cl). Our results reveal the presence of various communities in Archaea in lakes and a marked difference in this diversity between the depths sampled. In addition, the presence of a gene associated with nitrification, the amoA gene, was detected for the first time in a lacustral environment. This discovery allows us to assume the presence of Archaea nitrifiantes in lakes A and Cl.