A comparison of autotrophic (AD) and heterotrophic (HD) cathodic denitrification in a Microbial Fuel Cell (MFC) was made in this study. Denitrifying microbial consortia were developed from cow manure and soil and acclimatized under AD and HD conditions. The AD MFC supported the power output of 4.45Wm(-3) while removing nitrate nitrogen (NO3--N) at the rate of 0.118 kg NO3--Nm(-3) d(-1). Significant power output (3.02Wm(-3)) and nitrate removal rate (2.06 kg NO3--Nm(-3) d(-1)) were achieved in HD MFC. Further, 16S rDNA based community analysis revealed higher diversity in HDMFC. The genus Thauera and Pseudomonas were predominant in ADMFC while genus Klebsiella and Alkaliphilus were abundant in HDMFC. The abundance of the denitrifying genes namely narG, nirS, and nosZ were assessed with the help of quantitative PCR and presence of all the genes in both the conditions ensured the necessary molecular requirements for complete denitrification.