and have varying transmission dynamics that are informed by molecular epidemiology. This study aimed to determine the complexity of infection and genetic diversity of and throughout Papua New Guinea (PNG) to evaluate transmission dynamics across the country. In 2008-2009, a nationwide malaria indicator survey collected 8,936 samples from all 16 endemic provinces of PNG. Of these, 892 positive samples were genotyped at and , and 758 positive samples were genotyped at . The data were analyzed for multiplicity of infection (MOI) and genetic diversity. Overall, had higher polyclonality (71%) and mean MOI (2.32) than (20%, 1.39). These measures were significantly associated with prevalence for but not for . The genetic diversity of (: expected heterozygosity = 0.95, 0.85-0.98; : 0.78, 0.66-0.89) was higher and less variable than that of (: 0.89, 0.65-0.97). Significant associations of MOI with allelic richness (rho = 0.69, = 0.009) and expected heterozygosity (rho = 0.87, < 0.001) were observed for . Conversely, genetic diversity was not correlated with polyclonality nor mean MOI for . The results demonstrate higher complexity of infection and genetic diversity of across the country. Although shows a strong association of these parameters with prevalence, a lack of association was observed for and is consistent with higher potential for outcrossing of this species.