Background: The population structure of the causative agents of human malaria, Plasmodiumrnspecies including the most serious agent Plasmodium falciparum ( P.falciparum), depends onrnthe local epidemiological and demographic situations, such as the incidence of infected people,rnthe vector transmission intensity and migration of inhabitants (i.e. exchange between sites).Onernof the major characteristics of malaria parasites is their genetic diversity and an increasingrnnumber of studies have been reported on the population structure variation of P. falciparumrnbased on the polymorphism of merozoite surface protein (MSP) 1 and 2. Limited data howeverrnare available from Ethiopia.rnObjective: To evaluate the extent of genetic diversity of P falciparum in Kola-Shele in SouthrnWest of Ethiopia.rnMethods: Health facility based cross sectional study design was employed to determine thernprevalence of genetic diversity of P.falciparum in Kola-Shele area. Eighty-eight stored driedrnblood spot samples which were collected between September and December, 2008 were used.rnParasite DNA was extracted from the blood spot on to filter paper and analyzed by lengthrnpolymorphism following gel electrophoresis of DNA products from nested polymerase chainrnreactions targeted block 2 of msp-1 and block 3 of msp-2,including their allelic families:rnK1,MAD20,RO33 and FC27,3D7/IC1, respectively. Data entry was done using Microsoft Excelrnsheet and was double entered to verify accuracy; data was analyzed using SPSS for windows 16rnsoft ware (SPSS INC, Chicago, IL, USA).rnResults: The total number of alleles identified in MSP1 block 2 was 11, while 12 alleles werernobserved in MSP2 block 3.In MSP1, K1was found to be the predominant allelic type, carriedrnalone, with MAD20 and RO33 type. In MSP2, 3D7/IC was the most identified. Forty- three andrnsixty nine percent of isolates MSP1 and MSP2, respectively had high multiple genotypes andrnthe overall mean multiplicity of infection was 1.8 (95% CI: 1.48-2.04).rnConclusion: The Genetic diversity in P. falciparum field isolates in kolla-Shelle area were mixedrnand multiple infections were observed. K1 and 3D7/IC1 were the most predominant circulatingrnallelic families