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Background  Drug resistance is one of the main reasons of anti-malarial treatment failures and impedes malaria containment strategies. As single nucleotide polymorphisms (SNPs) have been found to correlate with anti-malarial drug resistance, the surveillance strategy includes continuous monitoring of known molecular markers and detection of new mutation patterns. With the introduction of artemisinin-based combination therapy, selection of specific patterns has been observed worldwide.    Methods  From March to June 2013, whole blood was collected on filter paper from microscopically malaria positive patients in Jimma zone (District), southwestern Ethiopia.  Plasmodium falciparum ,  Plasmodium vivax  and mixed infections were included. SNPs were investigated by conventional or real-time PCR, restriction fragment length pattern analysis or sequencing. Results were compared to molecular patterns from Ethiopian isolates in 2004, 2006 and 2008/9.    Results   Plasmodium falciparum ,  P. vivax , and mixed infections were molecularly confirmed in 177, 80, and 14 samples, respectively. In  P. falciparum , mutations in the  pfcrt ,  pfmdr 1 and  pfATP 6 (SERCA)  gene were investigated. Whereas the mutation in the  pfcrt  gene at codon 76 K was still found in 95.6 % of all samples, the  pfmdr 1  86 T mutation fell to 1.2 % (2/163) in 2013 compared to 9 % in 2008/9 and 86 % in 2006 ( P  <0.001). The  pfmdr 1  184 F mutation dominated with 100.0 % (172/172) in 2013. Sequencing of the recently reported PF3D7_1343700 kelch propeller domain showed no mutation at codon 476. First sequencing data of the  pvmdr 1  gene from Jimma region revealed a prevalence of the mutations 976 F and 1076 L in 72.7 % (16/23) and 100.0 % (19/19) of the isolates, respectively.    Conclusion  Since the introduction of artemether-lumefantrine (AL) in Jimma, Ethiopia, in 2006, the prevalence of certain SNPs associated with AL use has increased. Markers for chloroquine resistance in  P. vivax  were highly frequent. Continuous molecular and clinical surveillance are of paramount importance.    Electronic supplementary material  The online version of this article (doi:10.1186/s12936-015-0723-2) contains supplementary material, which is available to authorized users.

Molecular markers of anti-malarial drug resistance in southwest Ethiopia over time: regional surveillance from 2006 to 2013