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Background  Non-human primates have long been identified to harbour different species of  Plasmodium . Long-tailed macaques ( Macaca fascicularis ), in particular, are reservoirs for  P. knowlesi ,  P. inui ,  P. cynomolgi ,  P. coatneyi  and  P. fieldi . A previous study conducted in Sarawak, Malaysian Borneo, however revealed that long-tailed macaques could potentially harbour novel species of  Plasmodium  based on sequences of small subunit ribosomal RNA and circumsporozoite genes. To further validate this finding, the mitochondrial genome and the apicoplast caseinolytic protease M genes of  Plasmodium  spp. were sequenced from 43 long-tailed macaque blood samples.    Results  Apart from several named species of malaria parasites, long-tailed macaques were found to be potentially infected with novel species of  Plasmodium , namely one we refer to as “ P. inui -like.” This group of parasites bifurcated into two monophyletic clades indicating the presence of two distinct sub-populations. Further analyses, which relied on the assumption of strict co-phylogeny between hosts and parasites, estimated a population expansion event of between 150,000 to 250,000 years before present of one of these sub-populations that preceded that of the expansion of  P. knowlesi . Furthermore, both sub-populations were found to have diverged from a common ancestor of  P. inui  approximately 1.5 million years ago. In addition, the phylogenetic analyses also demonstrated that long-tailed macaques are new hosts for  P. simiovale .    Conclusions  Malaria infections of long-tailed macaques of Sarawak, Malaysian Borneo are complex and include a novel species of  Plasmodium  that is phylogenetically distinct from  P. inui . These macaques are new natural hosts of  P. simiovale , a species previously described only in toque monkeys ( Macaca sinica ) in Sri Lanka. The results suggest that ecological factors could affect the evolution of malaria parasites.    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1170-9) contains supplementary material, which is available to authorized users.

Malaria parasites of long-tailed macaques in Sarawak, Malaysian Borneo: a novel species and demographic and evolutionary histories