A sample of 204 skinks (Squamata: Scincidae) from 10 genera representing 24 species were collected from 10 different localities in New Guinea and examined for blood parasites. Hemogregarines, trypanosomes, microfilarial worms, and 8 infections showing 2 distinct morphological types of malaria parasites (Plasmodium sp.) were observed. Molecular sequence data, in the form of mitochondrial cytochrome b sequences from the Plasmodium infections, showed 2 distinct clades of parasites, 1 in Sphenomorphus jobiense hosts and 1 in Emoia spp., which correspond to the 2 morphotypes. There was substantial genetic variation between the 2 clades, as well as within the clade of Emoia parasites. Nearly half of the skinks sampled had green blood pigmentation, resulting from the presence of biliverdin in the plasma; however, only 1 of these lizards was infected with Plasmodium sp. and only 2 had any blood parasites. These preliminary results suggest a high degree of phylogenetic diversity but a very low prevalence of Plasmodium spp. infections in the skinks of this globally important biodiversity hot spot.