Internally Transcribed Spacer PCR: Basically you amplify spacer region of the bacterial rRNA. An informed guess make me suggest that since those regions are more important for size than for "meaning" they are likely to have relaxed evolutionary pressure, and are likely to change quickly (relatively), making them good target to differentiate between strains of similar organisms.
From http://biowww.net/detail-1294.html:
RAPD is random amplified polymorphic DNA The method is based on the Polymerase Chain Reaction (PCR) using short (usually 10 nucleotide) primers of arbitrary sequences. Polymorphism of amplified fragments are caused by: (1) base substitutions or deletions in the priming sites, (2) Insertions that render priming sites too distant to support amplification, or (3) insertions or deletions that change the size of the amplified fragment. (Bioinformatics Centre and Library, Central Plantation Crops Research Institute Kasaragod )
