The circumsporozoite genes and flanking sequences of the Ceylon, Gombak, London, NIH and Mulligan strains of the Plasmodium cynomolgi complex were isolated by molecular cloning and compared. About 11,000 bases of the Gombak clone were mapped in detail and found to have their exact counterparts in all the other strains. In contrast the epitope-encoding region, a 600-base sequence consisting of short tandem repeats, exhibited no homology with any of the other clones. These findings show that different regions of the circumsporozoite gene evolve in sharply different modes.