The present study demonstrates that two macaque malaria parasites naturally transmissible to humans, P. cynomolgi, and P. inui, exist among all the 7 sampled regional populations of wild long-tailed macaques. Specifically, P. cynomolgi showed distinctively and uniformly high prevalence in the macaques, except for the two populations from the Philippines. The low prevalence of Plasmodium in macaques from Zamboanga in the southern Philippines and Batangas in the northern Philippines does not suggest that host genetic differences are responsible, because long-tailed macaques in the latter geographic region are assigned to a uniquely different subspecies (M. f. philippensis) than those (M. f. fascicularis) inhabiting all other regions studied [29]. It is only recently confirmed that P. cynomolgi can also be transmitted to humans naturally and thus represents a potential new zoonotic malaria [14]. The observation of the high prevalence of P. cynomolgi in macaques from this study indicates the strong need of public advocacy in the affected areas.