The Lactobacillus plantarum commensal WCFS1 contains four prophage elements in its genome. Lp1 and Lp2 are two about 40-kb-long uninducible prophages that share closely related DNA packaging, head and tail genes defining a second lineage of pac-site Siphoviridae in L. plantarum, distinct from L. plantarum phage phig1e, but related to Bacillus phage SPP1 and Lactococcus phage TP901-1. Northern analysis revealed transcribed prophage genes exclusively near both attachment sites. Comparative genomics identified candidate lysogenic conversion genes (LCG) downstream of the lysis cassette and within the lysogeny module. Notable are genes with sequence similarities to putative LCG from Streptococcus pyogenes prophages and to a Bacillus plasmid. Both prophages harbored tRNA genes. R-Lp3 and R-Lp4 represent short prophage remnants; R-Lp3 abuts Lp2 and displays sequence links to cos-site Siphoviridae.