Paenibacillus profundus YoMME was isolated from the anodic biofilm of a sediment microbial fuel cell and recognized as one of the few exoelectrogenic Gram-positive bacteria, capable of transferring electrons extracellularly. Here, we report its draft genome sequence. The genome project is deposited at DDBJ/ENA/GenBank under the accession number JAJNBZ000000000.