Constructed wetlands form a unique ecosystem having plants, soil, microbes in which microorganisms play a vital role in the transformation and degradation of pollutants from wastewater. In the present study, French type two-stage vertical flow constructed wetland (VFCW) was used for the treatment of single household greywater (GW). Pilot-scale VFCW having sand and gravel as the filter substrate was constructed with Canna indica plantation for treating GW. To understand the pollutant removal mechanism in VFCW, microbial diversity and functional annotation was carried out by metagenomics analysis of sequences obtained from illumina platform. Efficiency of VFCW was measured with respect to water quality parameters like COD, BOD5, Total Nitrogen, Nitrate, Nitrite, Ammoniacal-N, ortho-phosphate and TOC from inlet and outlet of system. The removal efficiency was 90%, 93%, 34%, 26%, 89%, 68%, 80%, and 80% for COD, BOD5, Total Nitrogen, Nitrate, Nitrite, Ammoniacal-N, ortho-phosphate and TOC respectively. Microbial diversity was much more diversified and unique in VFCW compared to GW. Metagenomes exhibited Proteobacteria and Bacteroidetes as major phyla in GW whereas Actinobacteria, Proteobacteria, Nitrospirae abundance in VFCW layers. Total of 809 and 695 genus were found in VFCW and GW respectively with minimum abundance of 10 hits. From functional annotation of sequences, VFCW microbes have the potential to transform various aromatic and xenobiotic compounds along with the removal of pollutants present in the form of Carbon, Nitrogen, and Phosphorus. These data reveal French type VFCW can efficiently treat GW and with its own unique, variable habitat VFCW harbours diverse community of microorganisms that transform and degrade the pollutants in GW.