We report here the draft genome sequence of Paenibacillus polymyxa strain CCI-25, which displays strong antifungal and antibacterial activities in vitro. The genome encompasses nonribosomal peptide synthetases predicted to encode a tridecaptin, polymyxin, fusaricidin, an iturin-like synthetase, a lantibiotic similar to paenicidin A, as well as a type 1 polyketide synthase.