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Background  While Malaysia has had great success in controlling  Plasmodium falciparum  and  Plasmodium vivax , notifications of  Plasmodium malariae  and the microscopically near-identical  Plasmodium knowlesi  increased substantially over the past decade. However, whether this represents microscopic misdiagnosis or increased recognition of  P. knowlesi  has remained uncertain.    Methods  To describe the changing epidemiology of malaria in Sabah, in particular the increasing incidence of  P. knowlesi , a retrospective descriptive study was undertaken involving a review of Department of Health malaria notification data from 2012–2013, extending a previous review of these data from 1992–2011. In addition, malaria PCR and microscopy data from the State Public Health Laboratory were reviewed to estimate the accuracy of the microscopy-based notification data.    Results  Notifications of  P. malariae/P. knowlesi  increased from 703 in 2011 to 815 in 2012 and 996 in 2013. Notifications of  P. vivax  and  P. falciparum  decreased from 605 and 628, respectively, in 2011, to 297 and 263 in 2013. In 2013,  P. malariae/P. knowlesi  accounted for 62% of all malaria notifications compared to 35% in 2011. Among 1,082  P. malariae/P. knowlesi  blood slides referred for PCR testing during 2011–2013, there were 924 (85%)  P. knowlesi  mono-infections, 30 (2.8%)  P. falciparum , 43 (4.0%)  P. vivax , seven (0.6%)  P. malariae , six (0.6%) mixed infections, 31 (2.9%) positive only for  Plasmodium  genus, and 41 (3.8%)  Plasmodium -negative.  Plasmodium knowlesi  mono-infection accounted for 32/156 (21%) and 33/87 (38%) blood slides diagnosed by microscopy as  P. falciparum  and  P. vivax,  respectively. Twenty-six malaria deaths were reported during 2010–2013, including 12 with ‘ P. malariae/P. knowlesi ’ (all adults), 12 with  P. falciparum  (seven adults), and two adults with  P. vivax .    Conclusions  Notifications of  P. malariae/P. knowlesi  in Sabah are increasing, with this trend likely reflecting a true increase in incidence of  P. knowlesi  and presenting a major threat to malaria control and elimination in Malaysia. With the decline of  P. falciparum  and  P. vivax , control programmes need to incorporate measures to protect against  P. knowlesi , with further research required to determine effective interventions.    Electronic supplementary material  The online version of this article (doi:10.1186/1475-2875-13-390) contains supplementary material, which is available to authorized users.

Changing epidemiology of malaria in Sabah, Malaysia: increasing incidence of Plasmodium knowlesi