Methanogenic archaea may have been among earth earliest organisms and today play essential roles in a variety of anaerobic habitants. The present investigation was to study the methanogen population in estuarine sediments in the mouth of Manimuthar River at the Palk Strait and seasonal sampling was made. Most Probable number (MPN) of methanogenic archaea was determined in the period of one year(2009). The archaeal populations were found to be at the maximum of 1.1x105 MPNgm-1 of wet sample during the post-monsoon season. The correlation co efficient (r) values calculated between the methanogenic archaea and various physico chemical parameters in this nitrogen, sodium shows a high significant correlation to the MPN viz., n=18; r=0.976; and r=0.977 at; p<0.001 level respectively. Seasonal variation in the methanogenic population could be influenced by independent abiotic variables such as temperature, salinity, pH, electrical conductivity, nutrients and minerals. The investigation concluded that the methanogenic populations were highly influenced by physico chemical parameters in estuarine ecosystem. This is the first report in distribution of methanogens in this region.