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Background  The genetic diversity of  Plasmodium falciparum  has been extensively studied in various countries. However, limited data are available from Ethiopia. This study was conducted to evaluate the extent of genetic diversity of  P. falciparum  in Kolla-Shele, in the southwest of Ethiopia.    Methods  A total of 88 isolates from patients with uncomplicated  P. falciparum  attending Kolla-Shele Health Centre was collected from September to December, 2008. After extraction of DNA by Chelex® method, the samples were genotyped by using nested-PCR of  msp1  (block 2) and  msp2  (block 3) including their allelic families: K1, MAD20, RO33 and FC27, 3D7/IC1, respectively.    Results  Allelic variation in both  msp1  and  msp2  were identified in the 88 blood samples. For  msp1  67% (59/88) and  msp2  44% (39/88) were observed. K1 was the predominant  msp1  allelic family observed in 33.9% (20/59) of the samples followed by RO33 and MAD20. Of the  msp2  allelic family 3D7/IC1 showed higher frequency (21.5%) compared to FC27 (10.3%). A total of twenty-three alleles were detected; of which, eleven were from  msp2  and twelve from  msp2  genes. Fifty-nine percent of isolates had multiple genotypes and the overall mean multiplicity of infection was 1.8 (95% CI: 1.48-2.04). The heterozygosity index was 0.79 and 0.54for  msp1  and  msp2 , respectively. There was no statically significant difference in the multiplicity of infection by either age or parasite density (P > 0.05).    Conclusion  This genetic diversity study showed the presence of five allelic types in the study area, with dominance K1 in the  msp1  family and 3D7/IC1 in the  msp2  family. Multiple infections were observed in nearly 60% of the samples.    Electronic supplementary material  The online version of this article (doi:10.1186/s12936-015-0604-8) contains supplementary material, which is available to authorized users.

Genetic diversity of Plasmodium falciparum isolates based on MSP-1 and MSP-2 genes from Kolla-Shele area, Arbaminch Zuria District, southwest Ethiopia