How long has malaria been going on?
The answer to your question depends on the kind of malaria as well as how exactly you define ‘malaria’. The parasites which cause all forms of malaria, in humans as well as other mammals and birds, belong to a group called Plasmodium; scientists believe, based on genetic information, that this genus evolved around 130 million years ago, which is before the dinosaurs went extinct! These ancient ‘malaria’ parasites probably infected lizards; some types of malaria still infect reptiles today.
Plasmodium parasites have since evolved to infect primates, including humans; some scientists argue that this ‘jump’ has probably occurred several times in evolutionary history, whereas other suggest it has only happened once; the debate on this will likely continue for some time!
In terms of when human malaria first evolved, the four main types of malaria that infects humans are P. vivax, P. malariae, P. ovale and P. falciparum; the first three likely either co-evolved with humans or at least first became associated with infecting humans very soon after anatomically modern humans evolved. This dates these types of malaria back to the Middle Stone Age, which started around 300,000 years ago in Africa.
P. falciparum, on the other hand, probably crossed over much more recently, and the most up-to-date genetic evidence suggests that it evolved from a type of malaria which is found in gorillas. Estimates for when this transfer occurred are shaky at best, but it might have only been in the region of 10,000 years ago.
For more reading on the debate regarding the origin and evolutionary histories of Plasmodium as a whole and human forms of malaria more specifically, the following scientific articles may be a good place to start:
Joy, DA; Feng X, Mu J, Furuya T, Chotivanich K, Krettli AU, Ho M, Wang A, White NJ, Suh E, Beerli P & Su XZ, (2003). ‘Early origin and recent expansion of Plasmodium falciparum’, Science 300 (5617): 318–21
Liu, W; Y Li, GH Learn, RS Rudicell, JD Robertson, BF Keele, JN Ndjango, CM Sanz, DB Morgan, S Locatelli, MK Gonder, PJ Kranzusch, PD Walsh, E Delaporte, E Mpoudi-Ngole, AV Georgiev, MN Muller, GM Shaw, M Peeters, PM Sharp, JC Rayner & BH Hahn (2010), ‘Origin of the human malaria parasite Plasmodium falciparum in gorillas’, Nature 467.
Yotoko KSC & Elisei C (2006), ‘Malaria parasites (Apicomplexa, Haematozoea) and their relationships with their hosts: is there an evolutionary cost for the specialization?’, Journal of Zoological Systematics and Evolutionary Research 44 (4): 265–73