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Background  Habitat types can affect vector and pathogen distribution and transmission dynamics. The prevalence and genetic diversity of  Plasmodium  spp. in two eastern chimpanzee populations—Kalinzu Forest Reserve, Uganda and Issa Valley, Tanzania—inhabiting different habitat types was investigated. As a follow up study the effect of host sex and age on infections patterns in Kalinzu Forest Reserve chimpanzees was determined.    Methods  Molecular methods were employed to detect  Plasmodium  DNA from faecal samples collected from savanna-woodland (Issa Valley) and forest (Kalinzu Forest Reserve) chimpanzee populations.    Results  Based on a  Cytochrome - b  PCR assay, 32 out of 160 Kalinzu chimpanzee faecal samples were positive for  Plasmodium  DNA, whilst no positive sample was detected in 171 Issa Valley chimpanzee faecal samples. Sequence analysis revealed that previously known  Laverania  species ( Plasmodium reichenowi ,  Plasmodium billbrayi  and  Plasmodium billcollinsi ) are circulating in the Kalinzu chimpanzees. A significantly higher proportion of young individuals were tested positive for infections, and switching of  Plasmodium  spp. was reported in one individual. Amongst the positive individuals sampled more than once, the success of amplification of  Plasmodium  DNA from faeces varied over sampling time.    Conclusion  The study showed marked differences in the prevalence of malaria parasites among free ranging chimpanzee populations living in different habitats. In addition, a clear pattern of  Plasmodium  infections with respect to host age was found. The results presented in this study contribute to understanding the ecological aspects underlying the malaria infections in the wild. Nevertheless, integrative long-term studies on vector abundance,  Plasmodium  diversity during different seasons between sites would provide more insight on the occurrence, distribution and ecology of these pathogens.    Electronic supplementary material  The online version of this article (doi:10.1186/s12936-016-1476-2) contains supplementary material, which is available to authorized users.

A comparative molecular survey of malaria prevalence among Eastern chimpanzee populations in Issa Valley (Tanzania) and Kalinzu (Uganda)