During the life cycle, the parasite is haploid with the exception of a brief phase after fertilisation. In 1996 an International project was started to sequence the complete genome (23 Megabase) of P. falciparum. It is estimated that P. falciparum has about 5200 genes. The exact number depends upon the type of software used to search the databank. The nuclear genes are located on 14 chromosomes. Besides the nuclear genome, there is DNA in the mitochondria and in the apicoplast. The apicoplast is a left-over from a plastid of a green alga which once, in the course of evolution, is thought to have been an endosymbiont (cf. photosynthesis in the chloroplasts of plants). The apicoplast is transmitted via the macrogamete.

The Sanger Centre (UK), The Institute for Genomic Research (TIGR) in Rockville, Maryland (USA) and Stanford University in Palo Alto, California (USA) cooperated in this project. A large proportion of the costs are being borne by the Wellcome Trust Foundation and the NIH (National Institutes of Health, USA). A rough genetic map was produced by the end of 2000. A nearly complete genome sequence of the 3D7 reference strain of P. falciparum was published in the October 2002 issue of Nature.