There are increasing reports of severe disease exclusively associated with vivax malaria and this study presents the first one in Spain. The use of PCR excluded incompetent microscopy, cryptic mixed infections or sequestered P. falciparum reinforcing the need of using PCR as a new diagnostic tool to avoid default diagnosis of severe malaria as due to P. falciparum. The finding on increased expression levels of parasite genes likely involved in chloroquine resistance supports to furthering explore the potential of pvmdr1 and particularly pvcrt-o as molecular markers of severe disease in P. vivax.