Outcrossing potential between Plasmodium parasites is defined by the population-level diversity (PLD) and complexity of infection (COI). There have been few studies of PLD and COI in low transmission regions. Since the 1995-1998 Peruvian Amazon epidemic, there has been sustained transmission with < 0.5 P. falciparum and < 1.6 P. vivax infections/person/year. Using weekly active case detection, we described PLD by heterozygosity (H(e)) and COI using P. falciparum Pfmsp1-B2 and P. vivax Pvmsp3alpha. Not being homologous genes, we limited comparisons to within species. P. falciparum (N = 293) had low (H(e) = 0.581) and P. vivax (N = 186) had high (H(e) = 0.845) PLD. A total of 9.5% P. falciparum infections and 26.3% P. vivax infections had COI > 1. Certain allele types were in more mixed infections than expected by chance. The few appearances of new alleles could be explained by stochastic polymerase chain reaction detection or synchronization/sequestration. The results suggest propagation of mixed infections by multiple inocula, not super-infection, implying decade-long opportunity for outcrossing in these mixed infections.