Physical mapping of protozoan chromosomes has been transformed in recent years by the introduction of pulsed field gradient electrophor- esis (PFGE) (1 ). The chromosomes, which otherwise are too small to be detected in condensed form or mapped by conventional in situ hybridization methods, have a general size range that allows ready separation in agarose gels by PFGE. Reports of chromosomal separa- tions from different protozoans include examples from Leishmania (2 , 3 ), Giardia (4 ), Plasmodium (5 –8 ), and Trypanosoma (9 –11 ). Southern blots of PFGE separations readily serve to assign genetic markers on chromosomes. Methods have been developed to generate physical maps of individual chromosomes and to purify selected chrom- osome segments for the construction of recombinant DNA libraries.