Abstract: Detection of Plasmodium ssp. by analysis of extrachromosomal DNA. It has been found that the molecular composition, physical arrangements, and nucleotide sequences of the extrachromosomal plastid-like element and mitochondrial element are highly conserved in different Plasmodium ssp. The high degree of homology has been used to design genera-specific or species specific diagnostic assays with a low frequency of false negatives. Plastid and mitochondrial DNA sequences are disclosed. The use of the sequences is claimed for detection, prophylactic, and therapeutic treatment of Plasmodium ssp. infection in human or other animals.