Recent molecular studies indicate that Plasmodium ovale malaria is caused by two closely related species of protozoan parasites, thereby imposing new challenges for detection and species differentiation. This minireview explores the potential value of innovative methods for the molecular diagnosis of malaria with a strong emphasis on the discrimination and genotyping of P. ovale wallikeri and P. ovale curtisi as well as tools for the simultaneous detection of P. ovale sp. An update for the widely used NP-1993 to NP-2005 (SSU rRNA) protocols for all human malaria parasites is discussed.