A method using DNA fingerprinting to distinguish Plasmodium falciparum isolates has been developed using a clone, 7H8/6, isolated by screening a genomic expression library of the Malayan Camp strain with a monoclonal antibody. Unlike other P. falciparum DNA probes that contain internally repetitive sequences, this probe contains a single full-length open reading frame and lacks any repetitive sequences. Chromosome mapping located the hybridizing sequences to most chromosomes. 7H8/6 sequences are located at sites near the subtelomeric regions, although they are further from the telomeres than the subtelomeric repetitive sequences rep20. The probe gave multiple polymorphic bands on Southern blots of genomic DNA allowing all unrelated isolates tested to be readily distinguished. Hybridization patterns of parent and progeny from the genetic cross of two P. falciparum clones showed that most bands were inherited independently and no new bands were generated during the cross. This probe is useful for distinguishing isolates of P. falciparum and also for analyzing relationships between closely related isolates.